The impacts of substrate deformation on the resist filling characteristics were investigated both by experiment and by simulation for thermal imprint process. A Si mold with line and space pattern of 2 gm half pitch was used. The pattern area was surrounded by the flat area and its surface is as high as the top of the line pattern, that is, the concave mold is used. The mold pattern was transferred to a poly(methyl methacrylate) (PMMA) film on various thick Si substrates by the thermal imprint process. When the thin substrate of 200 gm thickness was used, no filling defects could be found. On the other hand, when the thick substrate of 1000 gm thickness was used, a large amount of filling defects were observed. It was clear that the filling defect could be suppressed by the substrate deformation. The substrate deformation was simulated by use of a simplified model. The substrate position, z(0), which is the boundary between the substrate and the PMMA film, was calculated. The formation of the filling defects could be explained by the substrate position, zo, quite well.