Charged particle beam system and methods

Disclosed is a charged particle beam system comprising a charged particle beam column having a charged particle source forming a charged particle beam, an objective lens and a first deflection system for changing a position of impingement of the charged particle beam in a sample plane. The system further comprises a sample chamber comprising a sample stage for holding a sample to be processed, and a controller configured to create and store a height map of a sample surface. The controller is further configured to dynamically adjust the objective lens of the charged particle beam in dependence on a position of impingement of the charged particle beam according to the height map.