diff --git a/make/common/templates/notary/server-config.json b/make/common/templates/notary/server-config.json
index dc8ffba31..faf06584c 100644
--- a/make/common/templates/notary/server-config.json
+++ b/make/common/templates/notary/server-config.json
@@ -22,7 +22,7 @@
             "realm": "$token_endpoint/service/token",
             "service": "harbor-notary",
             "issuer": "harbor-token-issuer",
-            "rootcertbundle": "/config/root.crt"
+            "rootcertbundle": "/etc/notary/root.crt"
         }
     }
 }
diff --git a/make/docker-compose.clair.tpl b/make/docker-compose.clair.tpl
index 4c652f115..b3429c042 100644
--- a/make/docker-compose.clair.tpl
+++ b/make/docker-compose.clair.tpl
@@ -41,7 +41,7 @@ services:
     depends_on:
       - postgres
     volumes:
-      - ./common/config/clair:/config:z
+      - ./common/config/clair/config.yaml:/etc/clair/config.yaml:z
     logging:
       driver: "syslog"
       options:  
diff --git a/make/docker-compose.notary.tpl b/make/docker-compose.notary.tpl
index 320ba9f8b..5633b6e02 100644
--- a/make/docker-compose.notary.tpl
+++ b/make/docker-compose.notary.tpl
@@ -15,7 +15,7 @@ services:
       - notary-sig
       - harbor-notary
     volumes:
-      - ./common/config/notary:/config:z
+      - ./common/config/notary:/etc/notary:z
     depends_on:
       - notary-db
       - notary-signer
@@ -34,7 +34,7 @@ services:
         aliases:
           - notarysigner
     volumes:
-      - ./common/config/notary:/config:z
+      - ./common/config/notary:/etc/notary:z
     env_file:
       - ./common/config/notary/signer_env
     depends_on:
diff --git a/make/photon/clair/docker-entrypoint.sh b/make/photon/clair/docker-entrypoint.sh
index 56f3affc1..f8e60defb 100644
--- a/make/photon/clair/docker-entrypoint.sh
+++ b/make/photon/clair/docker-entrypoint.sh
@@ -1,5 +1,4 @@
 #!/bin/bash
 set -e
-chown -R 10000:10000 /config
-sudo -E -H -u \#10000 sh -c "/dumb-init -- /clair2.0.1/clair -config /config/config.yaml"
+sudo -E -H -u \#10000 sh -c "/dumb-init -- /clair2.0.1/clair -config /etc/clair/config.yaml"
 set +e
diff --git a/make/photon/jobservice/start.sh b/make/photon/jobservice/start.sh
index 623e58b4e..607d44a4e 100644
--- a/make/photon/jobservice/start.sh
+++ b/make/photon/jobservice/start.sh
@@ -1,13 +1,4 @@
 #!/bin/sh
-if [ -d /etc/jobservice/ ]; then
-    chown -R 10000:10000 /etc/jobservice/ 
-fi
-if [ -d /var/log/jobs ]; then
-    chown -R 10000:10000 /var/log/jobs/
-fi
-if [ -d /var/log/jobs/scan_job ]; then
-    chmod +x /var/log/jobs/scan_job
-fi
 
 sudo -E -u \#10000 "/harbor/harbor_jobservice" "-c" "/etc/jobservice/config.yml"
 
diff --git a/make/photon/notary/server-start.sh b/make/photon/notary/server-start.sh
index 62083adb4..bbb38699e 100644
--- a/make/photon/notary/server-start.sh
+++ b/make/photon/notary/server-start.sh
@@ -1,3 +1,2 @@
 #!/bin/sh
-chown 10000:10000 -R /config
-sudo -E -u \#10000 sh -c "/usr/bin/env /migrations/migrate.sh && /bin/notary-server -config=/config/server-config.json -logf=logfmt"
+sudo -E -u \#10000 sh -c "/usr/bin/env /migrations/migrate.sh && /bin/notary-server -config=/etc/notary/server-config.json -logf=logfmt"
diff --git a/make/photon/notary/signer-start.sh b/make/photon/notary/signer-start.sh
index c6107dbac..4ddc97715 100644
--- a/make/photon/notary/signer-start.sh
+++ b/make/photon/notary/signer-start.sh
@@ -1,3 +1,2 @@
 #!/bin/sh
-chown 10000:10000 -R /config
-sudo -E -u \#10000 sh -c "/usr/bin/env && /migrations/migrate.sh && /bin/notary-signer -config=/config/signer-config.json -logf=logfmt"
+sudo -E -u \#10000 sh -c "/usr/bin/env && /migrations/migrate.sh && /bin/notary-signer -config=/etc/notary/signer-config.json -logf=logfmt"
diff --git a/make/photon/registry/entrypoint.sh b/make/photon/registry/entrypoint.sh
index 690a399f0..cbeb08bb1 100644
--- a/make/photon/registry/entrypoint.sh
+++ b/make/photon/registry/entrypoint.sh
@@ -2,12 +2,12 @@
 
 set -e
 
-if [ -d /etc/registry ]; then
-    chown 10000:10000 -R /etc/registry
-fi
+# The directory /var/lib/registry is within the container, and used to store image in CI testing.
+# So for now we need to chown to it to avoid failure in CI.
 if [ -d /var/lib/registry ]; then
     chown 10000:10000 -R /var/lib/registry
 fi
+
 if [ -d /storage ]; then
     if ! stat -c '%u:%g' /storage | grep -q '10000:10000' ; then
         # 10000 is the id of harbor user/group.
diff --git a/make/photon/ui/start.sh b/make/photon/ui/start.sh
index 6acfe61ec..db1385302 100644
--- a/make/photon/ui/start.sh
+++ b/make/photon/ui/start.sh
@@ -1,6 +1,3 @@
 #!/bin/sh
-if [ -d /etc/ui/ ]; then
-    chown -R 10000:10000 /etc/ui/ 
-fi
 sudo -E -u \#10000 "/harbor/harbor_ui"
 
diff --git a/make/prepare b/make/prepare
index 247d04d24..761d11cb9 100755
--- a/make/prepare
+++ b/make/prepare
@@ -19,6 +19,9 @@ if sys.version_info[:3][0] == 3:
     import configparser as ConfigParser
     import io as StringIO
 
+DATA_VOL = "/data"
+JOB_LOG_DIR = os.path.join(DATA_VOL, "job_logs")
+
 def validate(conf, args): 
     if args.ha_mode:
         db_host = rcp.get("configuration", "db_host")
@@ -68,6 +71,12 @@ def validate(conf, args):
     if project_creation != "everyone" and project_creation != "adminonly":
         raise Exception("Error invalid value for project_creation_restriction: %s" % project_creation)
 
+#To meet security requirement
+#By default it will change file mode to 0600, and make the owner of the file to 10000:10000
+def mark_file(path, mode=0o600, uid=10000, gid=10000):
+    os.chmod(path, mode)
+    os.chown(path, uid, gid)
+
 def prepare_ha(conf, args):
     #files under ha folder will have high prority
     protocol = rcp.get("configuration", "ui_url_protocol")
@@ -88,7 +97,7 @@ def prepare_ha(conf, args):
             if os.path.isfile(cert_path):
                 shutil.copy2(cert_path, shared_cert_path)
         #check if ca exsit
-        cert_ca_path = "/data/ca_download/ca.crt"
+        cert_ca_path = os.path.join(DATA_VOL, 'ca_download', 'ca.crt')
         shared_ca_path = os.path.join(base_dir, "ha", os.path.basename(cert_ca_path))
         if os.path.isfile(shared_ca_path):
             shutil.copy2(shared_ca_path, cert_ca_path)
@@ -138,16 +147,16 @@ def _get_secret(folder, filename, length=16):
             print("loaded secret from file: %s" % key_file)
         return key
     if not os.path.isdir(folder):
-        os.makedirs(folder, mode=0o600)
+        os.makedirs(folder)
     key = ''.join(random.choice(string.ascii_letters+string.digits) for i in range(length))  
     with open(key_file, 'w') as f:
         f.write(key)
         print("Generated and saved secret to file: %s" % key_file)
-    os.chmod(key_file, 0o600)
+    mark_file(key_file)
     return key
 
-def prep_conf_dir(root, name):
-    absolute_path = os.path.join(root, name)
+def prep_conf_dir(root, *name):
+    absolute_path = os.path.join(root, *name)
     if not os.path.exists(absolute_path):
         os.makedirs(absolute_path)
     return absolute_path
@@ -173,6 +182,10 @@ def delfile(src):
             itemsrc=os.path.join(src,item)
             delfile(itemsrc)
 
+if not os.path.exists(JOB_LOG_DIR):
+    os.makedirs(JOB_LOG_DIR)
+mark_file(JOB_LOG_DIR, mode=0o755)
+
 parser = argparse.ArgumentParser()
 parser.add_argument('--conf', dest='cfgfile', default=base_dir+'/harbor.cfg',type=str,help="the path of Harbor configuration file")
 parser.add_argument('--with-notary', dest='notary_mode', default=False, action='store_true', help="the Harbor instance is to be deployed with notary")
@@ -431,7 +444,7 @@ shutil.copyfile(os.path.join(templates_dir, "ui", "app.conf"), ui_conf)
 if auth_mode == "uaa_auth":
     if os.path.isfile(uaa_ca_cert):
         if not os.path.isdir(ui_cert_dir):
-            os.makedirs(ui_cert_dir, mode=0o600)
+            os.makedirs(ui_cert_dir)
         ui_uaa_ca = os.path.join(ui_cert_dir, "uaa_ca.pem")
         print("Copying UAA CA cert to %s" % ui_uaa_ca)
         shutil.copyfile(uaa_ca_cert, ui_uaa_ca)
@@ -491,8 +504,8 @@ if customize_crt == 'on' and openssl_installed():
     private_key_pem = os.path.join(config_dir, "ui", "private_key.pem")
     root_crt = os.path.join(config_dir, "registry", "root.crt")
     create_root_cert(empty_subj, key_path=private_key_pem, cert_path=root_crt)
-    os.chmod(private_key_pem, 0o600)
-    os.chmod(root_crt, 0o600)
+    mark_file(private_key_pem)
+    mark_file(root_crt)
 else:
     print("Copied configuration file: %s" % ui_config_dir + "private_key.pem")
     shutil.copyfile(os.path.join(templates_dir, "ui", "private_key.pem"), os.path.join(ui_config_dir, "private_key.pem"))
@@ -520,9 +533,6 @@ if args.notary_mode:
             create_root_cert(ca_subj, key_path=signer_ca_key, cert_path=signer_ca_cert)
             create_cert(cert_subj, signer_ca_key, signer_ca_cert, key_path=signer_key_path, cert_path=signer_cert_path)
             print("Copying certs for notary signer")
-            os.chmod(signer_cert_path, 0o600)
-            os.chmod(signer_key_path, 0o600)
-            os.chmod(signer_ca_cert, 0o600)
             shutil.copy2(signer_cert_path, notary_config_dir)
             shutil.copy2(signer_key_path, notary_config_dir)
             shutil.copy2(signer_ca_cert, notary_config_dir)
@@ -538,6 +548,10 @@ if args.notary_mode:
         shutil.copy2(os.path.join(notary_temp_dir, "notary-signer.key"), notary_config_dir)
         shutil.copy2(os.path.join(notary_temp_dir, "notary-signer-ca.crt"), notary_config_dir)
     shutil.copy2(os.path.join(registry_config_dir, "root.crt"), notary_config_dir)
+    mark_file(os.path.join(notary_config_dir, "notary-signer.crt"))
+    mark_file(os.path.join(notary_config_dir, "notary-signer.key"))
+    mark_file(os.path.join(notary_config_dir, "notary-signer-ca.crt"))
+    mark_file(os.path.join(notary_config_dir, "root.crt"))
     print("Copying notary signer configuration file")
     shutil.copy2(os.path.join(notary_temp_dir, "signer-config.json"), notary_config_dir)
     render(os.path.join(notary_temp_dir, "server-config.json"),
diff --git a/src/common/utils/notary/helper.go b/src/common/utils/notary/helper.go
index 63f9ae1cc..af7775a6e 100644
--- a/src/common/utils/notary/helper.go
+++ b/src/common/utils/notary/helper.go
@@ -36,7 +36,7 @@ import (
 )
 
 var (
-	notaryCachePath = "/etc/ui/notary-cache"
+	notaryCachePath = "/tmp/notary-cache"
 	trustPin        trustpinning.TrustPinConfig
 	mockRetriever   notary.PassRetriever
 )
diff --git a/src/ui/config/config.go b/src/ui/config/config.go
index 1035c562b..8b69c1e0a 100644
--- a/src/ui/config/config.go
+++ b/src/ui/config/config.go
@@ -38,8 +38,9 @@ import (
 )
 
 const (
-	defaultKeyPath       string = "/etc/ui/key"
-	defaultTokenFilePath string = "/etc/ui/token/tokens.properties"
+	defaultKeyPath                     = "/etc/ui/key"
+	defaultTokenFilePath               = "/etc/ui/token/tokens.properties"
+	defaultRegistryTokenPrivateKeyPath = "/etc/ui/private_key.pem"
 )
 
 var (
@@ -56,7 +57,7 @@ var (
 	AdmiralClient *http.Client
 	// TokenReader is used in integration mode to read token
 	TokenReader admiral.TokenReader
-
+	// defined as a var for testing.
 	defaultCACertPath = "/etc/ui/ca/ca.crt"
 )
 
@@ -189,6 +190,15 @@ func AuthMode() (string, error) {
 	return cfg[common.AUTHMode].(string), nil
 }
 
+// TokenPrivateKeyPath returns the path to the key for signing token for registry
+func TokenPrivateKeyPath() string {
+	path := os.Getenv("TOKEN_PRIVATE_KEY_PATH")
+	if len(path) == 0 {
+		path = defaultRegistryTokenPrivateKeyPath
+	}
+	return path
+}
+
 // LDAPConf returns the setting of ldap server
 func LDAPConf() (*models.LdapConf, error) {
 	cfg, err := mg.Get()
diff --git a/src/ui/config/config_test.go b/src/ui/config/config_test.go
index 67e50c6cb..b66e76cf4 100644
--- a/src/ui/config/config_test.go
+++ b/src/ui/config/config_test.go
@@ -185,6 +185,10 @@ func TestConfig(t *testing.T) {
 		t.Errorf("unexpected scan all policy %v", s)
 	}
 
+	if tokenKeyPath := TokenPrivateKeyPath(); tokenKeyPath != "/etc/ui/private_key.pem" {
+		t.Errorf("Unexpected token private key path: %s, expected: %s", tokenKeyPath, "/etc/ui/private_key.pem")
+	}
+
 	us, err := UAASettings()
 	if err != nil {
 		t.Fatalf("failed to get UAA setting, error: %v", err)
diff --git a/src/ui/service/token/authutils.go b/src/ui/service/token/authutils.go
index 18d2fa31a..79b5140a9 100644
--- a/src/ui/service/token/authutils.go
+++ b/src/ui/service/token/authutils.go
@@ -39,7 +39,7 @@ const (
 var privateKey string
 
 func init() {
-	privateKey = "/etc/ui/private_key.pem"
+	privateKey = config.TokenPrivateKeyPath()
 }
 
 // GetResourceActions ...
diff --git a/tests/testprepare.sh b/tests/testprepare.sh
index c55e852f0..f0f25d921 100755
--- a/tests/testprepare.sh
+++ b/tests/testprepare.sh
@@ -3,10 +3,10 @@ set -e
 cp tests/docker-compose.test.yml make/.
 
 mkdir -p /etc/ui
-cp make/common/config/ui/private_key.pem /etc/ui/.
+cp make/common/config/ui/private_key.pem /etc/ui/
 
 mkdir src/ui/conf
-cp make/common/config/ui/app.conf src/ui/conf/.
+cp make/common/config/ui/app.conf src/ui/conf/
 IP=`ip addr s eth0 |grep "inet "|awk '{print $2}' |awk -F "/" '{print $1}'`
 echo "server ip is "$IP
 sed -i -r "s/MYSQL_HOST=mysql/MYSQL_HOST=$IP/" make/common/config/adminserver/env