Disclosed are embodiments of an ion beam sample preparation and coating apparatus and methods. A sample may be prepared in one or more ion beams and then a coating may be sputtered onto the prepared sample within the same apparatus. A vacuum transfer device may be used with the apparatus in order to transfer a sample into and out of the apparatus while in a controlled environment. Various methods to improve preparation and coating uniformity are disclosed including: rotating the sample retention stage; modulating the sample retention stage; variable tilt ion beam irradiating means, more than one ion beam irradiating means, coating thickness monitoring, selective shielding of the sample, and modulating the coating donor holder.