Aren't SRTM files already fixed? I mean, an attempt has been made to fix them.
SRTMv4 has been 'fixed' according to the various step described in the link but there will still be problems. I've not encountered any in Outerra but I've no doubt they exist.
http://www.cgiar-csi.org/data/elevation/item/45-srtm-90m-digital-elevation-database-v41 I think you could get away with using Photoshop in png 16 bit format if you had auxillary dems that were not available to the folks who produced the v4. Blend the two terrains together. I'm not familiar with XNview -could you use that as a 3D viewer? Either way, you'd definitely need a 3D viewer to view your Photoshop work.
You could convert between the png and the native via Wilbur, 3DEM, or I could do it for you here painlessly via Global Mapper.
You could of course go track the areas down in Google Earth and eyeball their commercial terrain, and fix them manually but you'd need a 3D terrain package for that. I'd recommend Leveller, World Machine Pro or GeoControl. Wilbur is very capable and free!, but you're limted to 2D. Of the three, Leveller is the most paint friendly and there's a 64 bit version available now.
I've basically done this kind of thing before. I blended manually between our project data and real world data. You wouldn't need the Photoshop stage (but then you might well already have that app), but I'd recommend Leveller to do it.
A programmatic fix would be possible but I think they've already covered all those bases in v4 anyway.
If you feed me the lat long coords or links to files I could open them up, merge them and export them in a useful format. Any chance of posting some pics of the dodgy areas Kelvinr?
monks