ZEP resist patterns, which have been widely used in nanofabrication in research laboratories, are shrunk during an SEM observation. This shrinkage effect makes it challenging to accurately determine their original sizes. In this work, the shrinkage effect of electron beams on ZEP resist line-space patterns was explored by AFM measurement at different exposure doses. The results shown that the shrinkage happened at doses as low as 0.05 mC/cm 2 , and dramatically increased before being saturated at high doses of 16 -24 mC/cm 2 (at 30 keV). For patterns with the same height, a smaller pattern tended to undergo a bigger shrinkage. The heights of patterns also had a great impact on their shrinkages. In the saturation region at high does, the patterns were unchanged in isopropyl alcohol developer. The insolubility of the patterns suggested that the resist had changed to a negative tone, where the number of crosslinking sites of the resist was high, and caused the saturation of shrinkage. A new method for estimating of the original size was also introduced using a combination of SEM, EB exposure, and AFM.