You used the last release, didn't you? Sadly, that was a bad beta that is buggy as all hell. That thing screws up a MicroSD card pretty bad, but your computer should still be able to read it. Salvage what you can off of it, as DSOrganize does start corrupting everything on the card after awhile (I lost a couple saves that I, sadly, hadn't backed up, along with a game I hadn't.)
Otherwise you can just do a standard format (right click the drive for your MicroSD and format - do a full format, not a quick), or use the Panasonic SD Formatter.
If your computer isn't reading the MicroSD card though, you may have let DSOrganize wreak havoc for too long. I can't guarantee it didn't corrupt your MicroSD card beyond readability.