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One of the fundamental objectives of computer vision is to reconstruct a three-dimensional (3D) structure of objects from two-dimensional (2D) images. The basic idea of image focus is that objects at different distances from a lens are focused at different distances. Shape from Focus (SFF) is the problem of reconstructing the depth of the scene changing actively the optics of the camera until the point of interest is in focus. The point in focus gives information about its depth through the thin lens Gaussian law. An effective focus measure operator should be a high-pass filter. Usually, the variation of frequency components are not enough that focus measure could be computed pixel-wise, therefore, sum of pixels in small 2D windows are used for detecting the high frequency components. In this paper, we propose to use 3D windows instead of 2D windows for detecting the high frequency components in the images. The proposed algorithm using 3D window gives better depth map than the previous algorithms using 2D windows.