During short‐pulse laser crystallization of amorphous silicon on quartz, surface roughening occurs via the freezing of capillary waves excited in the silicon melt. The velocity and viscous damping of these capillary waves is computed and discussed. Volume change of the silicon during solidification appears to drive liquid silicon toward the last areas of solidification. Film thickness variation observed by transmission electron microscopy and atomic force microscopy shows increased film thickness at grain boundaries, and vertices of single pulse irradiated films. This effect is most pronounced within a narrow laser fluence regime wherein large lateral grain growth occurs. For 100 nm thick amorphous silicon films on quartz, this regime extends from approximately 520 to 560 mJ/cm2; standard deviation roughness can be as large as 40 nm. These effects have important implications for large area thin film transistor manufacturing.