Because of the interaction between probes and samples, pollutants in buffer solution or in the air would easily bind to probes and make the probe polluted, which might influence the morphological and mechanical measurements with atomic force microscopy. The polluted probes might transfer the pollutants onto the samples and thus change the surface ultrastructure of samples, or collect the deviated feedback signals to make the phantasm images. The former process is irreversible even if a new probe is employed, and the latter one is a reversible process as long as changing the used/polluted probe. Effects of polluted probes on morphological and mechanical characteristics of insect flight muscle and rat tail tendon collagen I fibers had been discussed in this study, in which, we constructed a series of methods to avoid/reduce the collecting of phantasm images and deviated mechanical information, such as changing the scanning direction and scanning force, replacing the new probes, or cleaning the polluted probes.