We report a method that involves using atomic force microscopy to estimate molecular interaction forces for bioapplications. Experimental parameters, comprising the labeling concentrations of tips and substrates and the loading rates of tips, were optimized for estimating molecular interaction forces for three pairs of model molecules (IgG/anti-IgG, BSA/anti-BSA, streptavidin/biotin). The estimated molecular interaction forces of IgG/anti-IgG, BSA/anti-BSA, and streptavidin/biotin were 121 +/- 3, 185 +/- 4, and 241 +/- 4 pN, respectively. The measured values were consistent and within the range of values reported in the literature. Estimation of molecular interaction forces in force-distance curves for bioapplication is still challenging. There are many potential bioapplications with further investigations. Providing additional screening reference for microsensing applications is one example. This method demonstrates favorable potential for effectively estimating molecular interaction forces for various applications of protein-ligand, antibody-antigen, ligand-receptor complexes, and other bioreactions. This method is also useful for studies of the structures and properties of molecular, cellular, and bacterial surfaces.