In the semiconductor industry, a device that can measure the surface-profile of photoresist is needed. Since the photoresist surface is very smooth and deformable, the device is required to measure vertical direction with nanometer resolution and not to damage it at the measurement. We developed the apparatus using multi-cantilever and white light interferometer to measure the surface-profile of thin film. But, this system with scanning method suffers from the presence of moving stage and systematic sensor errors. So, in this paper, an error separation approach used coupled distance sensors, together with an autocollimator as an additional angle measuring device, was consulted the potentiality for self-calibration of multi-cantilever. Then, according to this method, we constructed the experimental apparatus and do the measurement on the resist film. The results demonstrated the feasibility that the constructed multi-ball-cantilever AFM system combined with an autocollimator could measure the thin film with high accuracy.