Yes, of course.
I'll even make it step-by-step for you. Before formatting, back up everything on your card (by copying it to My Documents or wherever.)
1. Insert the SD Micro card into your reader and then insert the reader into your computer.
2. Go to My Computer and right-click the card (Verify it's the card you're right-clicking by double-clicking it first and seeing that it has your files on it. If it's not your card then you will cause serious damage. Make sure it's your card you right-clicked and you'll be fine.)
3. Click Format...
4. Keep all settings the same, but change the File System to FAT or FAT32 (either works) and change the Volume Label if you want. All the Volume Label is is a name for the card. It's not necessary to add one.
5. Click Start.
6. Once it's done, copy all the files you previously backed up back onto the card and you're done.
If this works, then enjoy. If it doesn't, then one or more of your files may be corrupted. Reformat your memory card and get new downloads of all your files, including the firmware, as some file somewhere on your card is messing things up. This will mean that you will lose your saves. Best of luck to you.