If you have access to plasma cleaning device - it might be used also to etch the surface, and in some cases to reduce the roughness, also in FTO.

However, if the surface roughness is critical for you, you might use other TCOs (ITO, AZO, etc.) instead of FTO. 

David,

I checked (air) plasma cleaning. Had almost no difference. After 30 minutes the roughness was reduced by about 2 nm (from~38 nm to ~36 nm). Do you have any specific guidelines for the plasma?