An inspection system with selectable apodization includes an illumination source configured to illuminate a surface of a sample, a detector configured to detect at least a portion of light emanating from the surface of the sample, the illumination source and the detector being optically coupled via an optical pathway of an optical system, a selectably configurable apodization device disposed along the optical pathway, wherein the apodization device includes one or more apodization elements operatively coupled to one or more actuation stages configured to selectably actuate the one or more apodization elements along one or more directions, and a control system communicatively coupled to the one or more actuation and configured to selectably control apodization of illumination transmitted along the optical pathway by controlling an actuation state of the one or more apodization elements.