In this paper, a novel modified Fourier transform method is proposed, which employs a fringe image and a flat image to eliminate the background and in the mean time facilitate the retrieval of the absolute phase map. Both the fringe and flat patterns are projected onto the object by a digital video projector. With the subtraction of the flat image from the fringe image, the background is completely removed and the spectrum overlapping in the frequency domain is prevented. The flat image is also employed for hole and shadow detection. Two cross-shaped markers are embedded in the flat and fringe image respectively for absolute phase retrieval. Experimental results showed that the proposed method produced better shape measurement results when measuring fast moving or changing objects, compared to the phase shifting method. The proposed method has the potential to boost the speed of our real-time 3-D shape measurement system to 120 fps with better measurement accuracy.