Hi Ryan,
you have to use md.inversion.cost_functions_coefficients and put zeros for the regions where you don't trust the data.
For example, if md.inversion.cost_functions = and you don't trust the regions where the velocity is smaller than 1 m/yr, you can do:
>> pos = find(md.inversion.vel_obs<1);
>> md.inversion.cost_functions_coefficients(pos,1) = 0;
You can also use an exp contour and use ContourToNodes to select the nodes that are inside a given region.
Let us know if you need help
Mathieu