A three dimensional molecular dynamics model is employed to simulate AFM-based lithography process. To investigate effects of tip geometry, three kinds of tip models are proposed: a cone-shape tip with a hemisphere at the end, a round-edged three sided pyramid tip with a hemisphere at the end and a sharp-edged three sided pyramid tip. These models simulate scratching behaviors of AFM tip at different scratching depths. Results showed that materials removal behavior and scratching forces were significantly affected by tip geometry, depending on the scratching depth and scratching directions. The specific energy using a sharp-edged three sided pyramid tip displayed a different behavior comparing to that using a round-edged three sided pyramid. However, scratching orientations exhibited no effects on the specific energy.