Below are the steps to create custom top in Oracle Application 

Step 1: Go to  APPL_TOP Dircetory in UNIX

Cd $APPL_TOP

Step 2: Create Custom Top Under APPL_TOP Dir

Mkdir CUSTNAME_TOP (Name of Directory)

Make sure all the files and Directories are same as Other Product Dir.

Step 3: Add Custom Top entry in APPLSYS.env file

Step 4: Login Oracle apps using SYSADMIN or AOL

Navigate: Applications->Register

Add your Custom top Entry Here

Application: CustomeApplication name

Short name: CUSTNAME

BasePath: CUSTNAME_TOP

Description: CustomApplication.

Step 5: Restart the Internal Concurrent Manager (ICM) for New Changes to take effect.

Step 6: Validate Custom Entry in

Select BASEPATH,PRODUCT_CODE,APPLICATION_SHORT_NAME

From fnd_application

Where application_Short_name like 'CUSTNAME_TOP%'