In this article, we introduce a novel shape from focus method to compute 3D shape of microscopic objects, based on modified-pixel intensities and Bezier surface approximations. A new and simple but effective focus measure is proposed. In our focus measure, the original intensities of a sequence of small neighborhood are modified by subtracting the maximum of the values of first and last frames. An initial depth map is calculated by finding the maximum of the pixel's focused energy and its corresponding frame number. Missing information between two consecutive frames, false depth detection, and enhancement of noise related intensities may provide inaccurate depth map. To overcome these problems and to produce an accurate depth map, we proposed Bezier surface approximation. The proposed method is tested using synthetic and real image sequences. The comparative analysis demonstrates the effectiveness of the proposed method.