Drilling carbon fiber isn't as difficult as one might think! Because carbon fiber is constructed of layers or plies of material this presents an opportunity (at each layer) for splintering or delamination. Drilling speed should be adjusted based on the diameter and depth of hole and some folks have also used certain tapes (i.e. electrical tape) at the hole site to help minimize splintering (primarily on the back side of the hole). Special drill bits designed specifically for carbon fiber can also be used to help eliminate delamination during drilling. These special drill bits can cost upwards of $100+ each and we have found that a quality carbide drill bit does the job just as well at a fraction the cost.
You will want to note that the dust from carbon fiber is conductive, and can migrate into electronics and short them out. Hence you must vacuum the dust frequently when machining to avoid causing damage to equipment. Carbon fiber dust can also irritate the skin (similar to working with fiberglass). It is good practice to wear gloves, a dust mask and always safety glasses when machining carbon fiber OR fiberglass composites.
Although it sounds complex, machining carbon fiber is not as difficult as it may seem from the first impression. Once you understand the basics, carbon fiber can be machined to the tight tolerances required without problems.