The source code mentioned above has functionality to remove tiny patches of voxels that you can seen in the surfaces. It can be done in Matlab as follows, using the svreg source code from the brainsuite website.
s=readdfs(surfacefile);
s=myclean_patch_cc(s);
sm=smooth_cortex_fast(s,.1,1000);
view_patch(sm);
We don’t have a command line utility for doing this, but the above mentioned matlab code should work.