Batch file to copy specific folders
SETLOCAL ensures that any environment variables you set don't affect the calling process's environment. It's like a sandbox for variables, directory changes, and other shell settings.

I usually use @ECHO instead of plain ECHOs so that if the @ECHO OFF is ever temporarily disabled (say, for debugging purposes), the echo statements don't produce needless noise in the output.

I also suggest using a loop to repeat the nearly-duplicate statements:

@ECHO OFF
SETLOCAL
:: variables
@ECHO This script takes the backup of file SwiftALM Important folders
SET /P source=Enter source folder Example D:\jboss6.1\server\swift:
SET /P destination=Enter Destination folder:
SET /P folder=Enter Folder name:

@ECHO folder=%folder%

MKDIR %destination%\%folder%
SET xcopy=xcopy /E/V/Q/F/H/I 

FOR /F %%s IN (conf lib deploy deployers) DO (
    echo %%s folder will be copied
    %xcopy% %source%\%%s %destination%\%folder%\%%s
    IF NOT ERRORLEVEL 1 @ECHO %%s folder has been copied.
)

@ECHO Files have been copied. Press enter to proceed.
PAUSE