In precision agriculture, 3D vision systems are becoming increasingly important. By applying different optical 3D vision techniques, the acquired 3D data can provide information regarding the most important phenotype features in every agricultural scenario. However, most of these 3D vision systems are expensive, except some of the triangulation techniques. In this study, we focus on estimating accurate shapes using shape from focus (SFF), which is a triangulation technique. Typically, the SFF system incurs significant errors from images, including noise. As a solution to this problem, a simple low-pass filter such as the Gaussian filter has generally been used in most studies. However, when a low filter is applied, the noise is depressed but the signals are also blurred, which results in inaccuracies regarding the depth map. In this study, the noise is depressed independently without losing the original signals, and the edge components, which play important roles in finding a focused surface, are enhanced using the independent component analysis (ICA). The edge signals are amplified with a simple basis vector correction in the IC vector space. The experiments are implemented with simulated objects and real objects. The experimental results demonstrate that the obtained accuracy is comparable to that of existing methods.