For reference, I am a student worker at the local college with what I would expect to have the skills of a semi-skilled hobbyist. Also, I am using a Tormach 1100MX, Fusion 360, and a drilling bit with a 6in flute.

Into the problem, I am machining holes through three-inch segments of copper for use in Ph.D. experimentation; therefore, the closer to perfection the better. The end goal is to have 8 individual blocks of copper that must align perfectly with one another, all with the holes in the center. I have been using Fusion360 to model this and mill with a Tormach 1100MX, aligning the stock with a machinist square, and using a probe to find my WCS. No matter how accurately I have measured or trued my pieces up the mill cannot accurately drill through the centroids of these pieces. After realizing that the pieces I had cut were not lining up I tried several things to check my work, the addition/subtraction of coolant, using a pilot hole with a center drill bit, and slowing my plunge rate. I expected these pieces to have much higher accuracy than they were coming out. I have tried everything I know, and I am out of ideas now. If any skilled machinist can lend some much-needed knowledge, it would be greatly appreciated.