Cosmic ray muon radiography which has good penetration ability and is sensitive to high-Z materials, is an effective method to detect shielded nuclear materials. This paper summarizes methods developed to process muon radiography in Tsinghua University. The methods include detector data correction, reconstruction algorithms (maximum likelihood scattering, MLS, and the maximum likelihood scattering and displacement, MLSD) acceleration, and the modification of the normalized mean absolute distance measure (NMADM) into a picture comparison binarization method (PCBM) which is more suitable for cosmic ray muon radiographs. Simulations demonstrate that all these methods give excellent results, so that cosmic muon radiography can become more widely used.