If I'm understanding you right, you're gonna get U-shaped cuts. You're stepping over an 1/8" with a 1/8" ball mill. To control the finish and get rid of the "U", change your step over to something really small. Instead of 1/8", try like .002-.003 and look. From there, you just tighten that up to obtain a good finish. Keep in mind too, MC verify is not the most detailed depiction, but it can keep you out of trouble.
Are these 3D cuts? I'm not sure what your part looks like.