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The easiest way to do this would be to backup what you want to keep from the memory card onto a PC then simply format the memory card with the phone:
Main Menu > Settings > Storage > Unmount SD Card > Format SD Card.
This will clear all data that has been added to the card then you can simply restore the data you want from the PC.
Do you have any applications that you have installed that you wish to keep? Other wise it would just be media content you have added that you would backup and formatting the memory card will then not cause any problems.
Then you would be fine to run a format of the SD Card through the phone to tidy this up.
Thanks alot!!