I have changed the Keep Tool Down within to 50% on the Cut Parameter Page and cahnged the Containment to Inside and it has seemed to have eliminated all of the gouges. Thanks everyone for such the fast and helpful reponses.

I am new to the surface machining and not sure if i have this part setup right or if i am doing the type of operation. I have attached Pictures of my Mastercam file showing all of the settings along with the result of the actual machining. I have also attached parasolids of the part after the roughing operations (just linear toolpaths, worked great) and after the final machining. The starting stock size is a 3/8" thick plate 6 1/2" x 10 1/2". The actual mastercam file is too large for me to add it to the post. Any help in figuring out how to prevent the goughes would be greatly apprecated. If anyone needs more information please let me know. Mastercam & Pics.pdf Part.zip