An improved method of directing a charged particle beam that compensates for the time required for the charged particles to traverse the system by altering one or more of the deflector signals. According to one embodiment of the invention, a digital filter is applied to the scan pattern prior to digital-to-analog (D/A) conversion in order to reduce or eliminate over-shoot effects that can result from TOF errors. In other embodiments, analog filters or the use of signal amplifiers with a lower bandwidth can also be used to compensate for TOF errors. By altering the scan pattern, over-shoot effects can be significantly reduced or eliminated.