A wide variety of three dimensional (3D) measurement systems that can extract shape information’s with sub millimetric accuracy is available in the industry. However, they generally are of macroscopic size and measuring on confined areas is not feasible. To miniaturize such systems, the step proposed is the integration of flexible image guides combined with compact optical probes. This miniaturization process is tested on an active stereoscopic measurement system. In the projection channel of the system, a digital micro-mirror device (DMD) generates structured binary patterns from an incoherent white light source and injects them into a first image guide. Then, a compact optical system projects the pattern on the measurement area. The same configuration principle is applied to the acquisition channel and allows the capture of the measurement area through a second image guide and finally to a digital camera. In this miniaturized system, image guides have lower resolution than in standard imaging devices. Indeed they are equivalent of 70k pixels devices to compare to the almost 800k pixels of the DMD and camera. That implies lower axial and lateral resolutions and consequently the shape reconstruction method must be carefully chosen. In this paper, several reconstruction strategies such as tuning the projected patterns frequency and also phase-shfit versus gray code based methods were compared considering the best axial resolution criteria.