In some embodiments, data is received defining a plurality of shot groups that will be delivered by a charged particle beam writer during an overall time period, where a first shot group will be delivered onto a first designated area at a first time period. A temperature of the first designated area at a different time period is determined. In some embodiments, the different time period is when secondary effects of exposure from a second shot group are received at the first designated area. In some embodiments, transient temperatures of a target designated area are determined at time periods when exposure from a shot group is received. An effective temperature of the target area is determined, using the transient temperatures and applying a compensation factor based on an amount of exposure received during that time period. A shot in the target shot group is modified based on the effective temperature.