In the pack and go window you can specify the path where you need to copy/move the file and then delete the original folder (this would be good if files are in same folder).
The option might be to use a macro to move your files but there is no direct option.
Thanks Deepak for your suggestion,
But my original folder contains lots of solidworks files, (may be about 500) and it is very difficult to find out one by one file required to complete that assemby.
Please suggest me if any one is having any other option.