Systems and methods are provided for dynamically compensating position errors of a sample. The system can comprise one or more sensing units configured to generate a signal based on a position of a sample and a controller. The controller can be configured to determine the position of the sample based on the signal and in response to the determined position, provide information associated with the determined position for control of one of a first handling unit in a first chamber, a second handling unit in a second chamber, and a beam location unit in the second chamber.