Noncontact atomic force microscopy (AFM) has recently progressed tremendously in achieving atomic resolution imaging through the use of small oscillation amplitudes and well-defined modification of the tip apex. In particular, it has been shown that picking up simple inorganic molecules (such as CO) by the AFM tip leads to a well-defined tip apex and to enhanced image resolution. Here, we use the same approach to study the three-dimensional intermolecular interaction potential between two molecules and focus on the implications of using molecule-modified AFM tips for microscopy and force spectroscopy experiments. The flexibility of the CO at the tip apex complicates the measurement of the intermolecular interaction energy between two CO molecules. Our work establishes the physical limits of measuring intermolecular interactions with scanning probes.