Studying physical properties of nanoscale materials has gained a significant attention owing to their applications in the fields such as electronics, medicine, pharmaceutical industry, and materials science. However, owing to size constraints, number of techniques that measures physical properties of materials at nanoscale with a high accuracy and sensitivity is limited. In this context, development of atomic force microscopy (AFM) based techniques to measure physical properties of nanomaterials has led to significant advancements across the disciplines including chemistry, engineering, biology, material science and physics. AFM has recently been utilized in the quantification of physical-chemical properties such as electrical, mechanical, magnetic, electrochemical, binding interaction and morphology, which are enormously important in establishing structure-property relationship. The overarching objective of the investigations discussed here is to gain quantitative insights into the factors that control electrical and mechanical properties of nano-dimensional organic materials and thereby, potentially, establishing reliable structure-property relationships particularly for organic molecular solids which has not been explored enough. Such understanding is important in developing novel materials with controllable properties for molecular level device fabrication, material science applications and pharmaceutical materials with desirable mechanical stability. First, we have studied electrical properties of novel silver based organic complex in which, the directionality of coordination bonding in the context of crystal engineering has been used to achieve materials with structurally and electrically favorable arrangement of molecules for an enhanced electrical conductivity. This system have exhibited an exceptionally high conductivity compared to other silver based organic complexes available in literature. Further, an enhancement in conductivity was also observed herein, upon photodimerization and the development of such materials are important in nanoelecrtonics. Next, mechanical properties of a wide variety of nanocrystals is discussed here. In particular, an inverse correlation between the Young’s modulus and atomic/molecular polarizability has been demonstrated for members of a series of macro- and nano-dimensional organic cocrystals composed of either resorcinol (res) or 4,6-di-X-res (X = Cl, Br, I) (as the template) and trans-1,2-bis(4-pyridyl)ethylene (4,4’-bpe) where cocrystals with highly-polarizable atoms result in softer solids. Moreover, similar correlation has been observed with a series of salicylic acid based cocrystals wherein, the cocrystal former was systematically modified. In order to understand the effect of preparation method towards the mechanical properties of nanocrystalline materials, herein we have studied mechanical properties of single component and two component nanocrystals. Similar mechanical properties have been observed with crystals despite their preparation methods. Furthermore, size dependent mechanical properties of active pharmaceutical ingredient, aspirin, has also been studied here. According to results reduction in size (from millimetre to nanometer) results in crystals that are approximately four fold softer. Overall, work discussed here highlights the versatility of AFM as a reliable technique in the electrical, mechanical, and dimensional characterization of nanoscale materials with a high precision and thereby, gaining further understanding on factors that controls these processes at nanoscale.