Systems, control subsystems, and methods for projecting an electron beam onto a specimen are provided. One system includes a stage configured to move the specimen with a non-uniform velocity. The system also includes a projection subsystem configured to project the electron beam onto the specimen while the stage is moving the specimen at the non-uniform velocity. In addition, the system includes a control subsystem configured to alter one or more characteristics of the electron beam while the projection subsystem is projecting the electron beam onto the specimen based on the non-uniform velocity. One method includes moving the specimen with a non-uniform velocity and projecting the electron beam onto the specimen during movement of the specimen. In addition, the method includes altering one or more characteristics of the electron beam during projection of the electron beam onto the specimen based on the non-uniform velocity.