Clouds strongly influence three-dimensional aerosol distributions by 1) wet scavenging and subsequent deposition to the earth's surface, and 2) processing and subsequent release to the atmosphere by evaporation processes. In this study, physically detailed size-dependent representations of below-cloud and in-cloud scavenging for mixed phase clouds are introduced into the ECHAM5-HAM global climate model. As well, a stratiform cloud aerosol processing scheme is extended to convective clouds. Below-cloud impaction scavenging is found to contribute strongly to the global and annual mean mass deposition for sulfate (14%), black carbon (13%), particulate organic matter (10%), sea salt (23%), and dust (24%). The modeled global mean aerosol optical depth, and sea salt burden are reduced by about 15% for the more vigorous size-dependent parameterization of below-cloud scavenging by rain and snow. In stratiform clouds, aerosol mass is found to be primarily (>90%) scavenged by cloud nucleation processes for all aerosol species, except for dust (50%). Uncertainties in the representation of in-cloud scavenging processes change the predicted annual, global mean aerosol mass burdens by 20 to 30%, and change the predicted aerosol mass concentrations by up to one order of magnitude in the middle troposphere where mixed phase clouds exist. Closer agreement with observations of black carbon profiles from aircraft is found for the new in-cloud scavenging scheme. Convective and stratiform clouds contribute about equally to the global, annual mean aerosol processing, but wet deposition is primarily attributed to stratiform clouds (75%). Sulfate and carbonaceous aerosols undergo 1-3 cloud cycles before deposition. Aerosol burdens and optical depth (AOD) increase by a factor of 3-5 with the explicit representation of cloud/precipitation evaporation. Revised sea salt emissions and more vigorous in-cloud impaction scavenging reduce the AOD by a factor of three to give closer agreement with satellite retrievals. Observed marine boundary layer accumulation mode size distributions, and vertically integrated aerosol size distributions from AERONET observations are more closely approximated with the aerosol processing scheme than for the standard ECHAM5-HAM.