Geometric models often contain small features that we would like to remove, including small extrusions and holes. Feature removal can be desirable for many reasons, including finite element simulation, analysis of feature purpose and so on. In this study, an algorithm based on level set method is proposed to remove the small features. First, we initialize the zero level set in such a way that the zero level set includes the input model. And then the zero level set evolves towards the input model based on a novel speed function. When zero level set stops moving, a simplified model without small features can be got. The method receives approval from the experimental results.