Given that anodising is an electrochemical process, can areas be masked or holes plugged to prevent coverage of an area?

eg. To create letters or symbols on a surface or to prevent buildup in machined bores or threads.

Yes, sections of a part can be masked. Flat areas can sometimes be more difficult to mask; holes and bores can usually be masked without too much difficulty. Lettering may be accomplished more satisfactorily either by casting them into the part or using laser engraving after anodising.