Based on the microscale 3D point cloud projection with a digital micromirror device (DMD) and a microlens array (MLA) developed recently, we explore the capabilities of this specific type of 3D projection in 3D lithography with femtosecond light in this study. Unlike 3D point cloud projection with UV continuous light demonstrated before, high accuracy positioning between the DMD and the MLA is required to have rays simultaneously arrive at the designed voxel positions to induce two-photon absorption with femtosecond light. Because of this additional requirement, a new positioning method through direct microscope inspection of the relative positions of the DMD and the MLA is developed in this study. Because of the usage of a rectangular MLA, around four rays can arrive at each projecting voxel at the same time. Thus, to the best of our knowledge, a new algorithm for determining the pixel map on the DMD to the 3D point cloud projection with a femtosecond laser is also developed. It is observed that a very long exposure time is required to generate 3D patterns with the new 3D projection scheme because of the very limited number of rays used for projecting each voxel with the new algorithm. It is also found that 3D structures with desired shapes should be projected far away from the MLA (∼15f to 30f, with f being the focal distance of the MLA) in the 3D lithography with this femtosecond 3D point cloud projection. For patterns projected closer than 10f, shapes are distorted because of unwanted voxels cured with the 3D projection technique using a DMD and MLA.