High throughput, low inner working angle (IWA) phase masks coronagraphs are essential to directly image and characterize (via spectroscopy) earth-like planets. However, the performance of low-IWA coronagraphs is limited by residual pointing errors and other low-order modes. The extent to which wavefront aberrations upstream of the coronagraph are corrected and calibrated drives coronagraphic performance. Addressing this issue is essential for preventing coronagraphic leaks, thus we have developed a Lyot-based low order wave front sensor (LLOWFS) to control the wavefront aberrations in a coronagraph. The LLOWFS monitors the starlight rejected by the coronagraphic mask using a reflective Lyot stop in the downstream pupil plane. The early implementation of LLOWFS at LESIA, Observatoire de Paris demonstrated an open loop measurement accuracy of 0.01 λ/D for tip-tilt at 638 nm when used in conjunction with a four quadrant phase mask (FQPM) in the laboratory. To further demonstrate our concept, we have installed the reflective Lyot stops on the Subaru Coronagraphic Extreme AO (SCExAO) system at the Subaru Telescope and modified the system to support small IWA phase mask coronagraphs (< 1λ/D) on-sky such as FQPM, eight octant phase mask, vector vortex coronagraph and the phase induced amplitude apodization complex phase mask coronagraph with a goal of obtaining milli arc-second pointing accuracy. Laboratory results have shown the measurement of tip, tilt, focus, oblique and right astigmatism at 1.55 μm for the vector vortex coronagraph. Our initial on-sky result demonstrate the closed loop accuracy of < 7 x 10-3 λ/D at 1.6 μm for tip, tilt and focus aberrations with the vector vortex coronagraph.