The Measurement Of Pollution In The Troposphere (MOPITT) instrument, which will be launched on the Terra spacecraft, is designed to measure the tropospheric CO and CH4 at a nadir-viewing geometry. The measurements are taken at 4.7 micrometer in the thermal region, and 2.3 and 2.2 micrometer in the solar region for CO mixing ratio retrieval, CO total column amount and CH4 column amount retrieval, respectively. To ensure the required measurement accuracy, it is critical to identify and remove any cloud contamination to the channel signals. In this study, we develop an algorithm to detect the cloudy pixels, to reconstruct clear column radiance for pixels with partial cloud covers, and to estimate equivalent cloud top positions under overcast conditions to enable CO profile retrievals above clouds. The MOPITT channel radiances, as well as the first guess calculations, are simulated using a fast forward model with input atmospheric profiles from ancillary data sets. The precision of the retrieved CO profiles and total column amounts in cloudy atmospheres is within the expected plus or minus 10% range. Validations of the cloud detecting thresholds with MODIS Airborne Simulator (MAS) data and MATR (MOPITT Airborne Test Radiometer) measurements are also carried out and will be presented separately.