Theory and theoretical simulation methods of Scanning Probe Microscopy including Scanning Tunneling Microscopy, and various kinds of Atomic Force Microscopy are reviewed with recent results. The topics introduced here are the method for the STM Simulation, effect of the dissipation on the tunneling current as well as the method for the theoretical simulation of the Atomic Force Microscopy in water. We presented two methods based on the classical molecular dynamics and 3D Reference Interaction Site Method (3D-RISM). Some remarkable properties of the 3D force map of mica in water and the effect of the local charging of the sample on the water mediated force are discussed.