+1 for Netfab. There's a built in function to do exactly what you want and it even puts in the surface for the split.
There's a post on this list somewhere that has a good tutorial of various tools to use to clean up scans that includes Netfab.
I just installed netfabb basic 4.9.2 and it seems every "cut" option in the program is limited to the "Pro" version. Unless I'm missing something it appears the free basic version no longer has the cutting feature. It was the only thing I downloaded it for too.
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