For effective endoscopic diagnosis and treatment, size measurement and shape characterization of lesions, such as tumors, is important. For this purpose, 3D endoscopic systems based on active stereo to measure the shape and size of living tissue have recently been proposed. In those works, a large problem is the degree of reconstruction instability due to image blurring caused by the strong subsurface scattering common to internal tissue. To reduce this instability problem, using a coarse pattern for structured light is an option, however it reduces the resolution of the acquired shape information. In this paper, we tackle these shortcomings by developing a new micro pattern laser projector to be inserted in the scope tool channel. There are hardware and software contributions in the paper. First, the new projector uses a Diffractive Optical Element (DOE) instead of a single lens which we proposed to solve the off-focus blur. Second, we propose a new line-based grid pattern with gap coding to counter the subsurface scattering effect. The proposed pattern is a coarse grid pattern so that the grid features are not blurred out by the subsurface scattering. Third, to increase shape resolution of line-based grid pattern, we propose to use a multiple shape data registration technique for the grid-structured shapes, which are acquired sequentially by small motions, is proposed. Quantitative experiments are conducted to show the effectiveness of the method followed by a demonstration using real endoscopic system.