If the scanner can read codes then it should be able to clear them. It will reset you system readiness tests and the codes will keep coming back everytime the cat efficiency test runs.
I don't think SLP will tune a cat-less car for the street after what the EPA did to caspers
http://www.epa.gov/oecaerth/resource...per-fcsht.html most companies won't mess with cheating OBD2 emmissions.