In this paper, the new method for OCT images denoizing based on empirical mode decomposition (EMD) is proposed. The noise reduction is a very important process for following operations to analyze and recognition of tissue structure. Our method does not require any additional operations and hardware modifications. The basics of proposed method is described. Quality improvement of noise suppression on example of edge-detection procedure using the classical Canny's algorithm without any additional pre- and post-processing operations is demonstrated. Improvement of rawsegmentation in the automatic diagnostic process between a tissue and a mesh implant is shown.