Some minor improvements:

• Since you have @echo off at the top, you don't need the @ in @echo folder=%folder%

• It looks like you doubled echo in this command by mistake: echo echo conf folder will be copied

• It would be good to add some blank lines to separate related blocks and improve readability

With the above suggestions applied it becomes:

@echo off
:: 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:
set xcopy=xcopy /E/V/Q/F/H/I 

echo folder=%folder%
mkdir %destination%\%folder%

echo conf folder will be copied
%xcopy% %source%\conf %destination%\%folder%\conf
echo conf folder is copied

echo lib folder will be copied
%xcopy% %source%\lib %destination%\%folder%\lib
echo lib folder is copied

echo deploy folder will be copied
%xcopy% %source%\deploy %destination%\%folder%\deploy
echo deploy folder is copied

echo deployers folder will be copied
%xcopy% %source%\deployers %destination%\%folder%\deployers 
echo deplyers folder is copied

echo files will be copy press enter to proceed
pause

Some minor improvements:

• It looks like you doubled echo in this command by mistake: echo echo conf folder will be copied

• It would be good to add some blank lines to separate related blocks and improve readability

With the above suggestions applied it becomes:

@echo off
:: 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:
set xcopy=xcopy /E/V/Q/F/H/I 

echo folder=%folder%
mkdir %destination%\%folder%

echo conf folder will be copied
%xcopy% %source%\conf %destination%\%folder%\conf
echo conf folder is copied

echo lib folder will be copied
%xcopy% %source%\lib %destination%\%folder%\lib
echo lib folder is copied

echo deploy folder will be copied
%xcopy% %source%\deploy %destination%\%folder%\deploy
echo deploy folder is copied

echo deployers folder will be copied
%xcopy% %source%\deployers %destination%\%folder%\deployers 
echo deplyers folder is copied

echo files will be copy press enter to proceed
pause