Welcome to Android Forums, Anand.
That's an easy one. Mount your phone in storage mode and then on your PC make sure you have it set to display hidden files (on XP tools>folder options>view tab and check the button that says show hidden files, on Vista/Win7 organize>folder and search options>view tab ... same button). Then copy all the files and folders to a backup folder on your PC.
Turn off Storage mode then on the phone go to menu>settings>storage and unmount the SD card. Depending on phone model you may have to shut down the phone to replace the card. However you need to do it, remove the old card and put the new one in. The reverse the process. Mount the phone as storage with the new card in it and copy all the files in the backup folder to the phone. Reboot the phone and you should be good.