The importance of studying the physico-chemical properties of nano-dimensional materials has gained significant attention in the fields of semiconductors, pharmaceuticals, materials science, and atmospheric chemistry owing to the differences in physical properties between macro- and nano-dimensional solids. Nonetheless, direct studies of physical properties of materials at nanoscale is limited in part due to their inherent size constraints and experimental limitations. However, development of atomic force microscopy (AFM) led to the implementation of methods to characterize a wide range of physical properties, including – but not limited to – mechanical properties, electrical properties, viscoelastic properties, and surface tension. Herein, the dissertation focuses on AFM-based method development for characterization of atmospheric particles as well as understanding the relationship between structure and physical properties of organic solids at both macro- and nano-dimensions. In the atmospheric chemistry realm, the combined aerosol effect on the climate and environment has significant uncertainty in part due to lack of direct characterization of their physico-chemical properties. The difficulty in assessing the physical and chemical properties arises due to the presence of diversified aerosol sources, which in turn influences the size, morphology, phase states and chemical compositions. Sea spray aerosols (SSAs) are the second-largest source of aerosols in the atmosphere. Studying SSAs – especially in submicrometer-dimensions – requires high-resolution microscopy techniques such as AFM. AFM can be used for imaging of individual aerosols, quantifying organic volume fraction for core-shell morphologies, measuring water uptake, quantifying surface tension of individual droplets, and measuring mechanical and viscoelastic properties of materials. Herein, we employed AFM-based morphology and force spectroscopy studies to correlate the 3D morphology, phase state, and viscoelastic properties of selected single-component chemical systems found in sea spray aerosol (SSA). We established a quantitative framework toward differentiation of the solid, semisolid and liquid phase states of individual particles by utilizing both relative indentation depth (RID) and viscoelastic response distance (VRD) data obtained from the force−distance plots. Moreover, we established a semi-quantitative and quick phase assessment by measuring the aspect ratio (AR) that refers the extent of particle spreading as a result of impaction. Overall, the established AFM-based quantitative and semi-quantitative phase identification method can be utilized to assess the phases of aerosols irrespective of chemical identity. Next, we investigated the factors that may control the electrical and mechanical properties of pharmaceutical and organic semiconducting materials in nano- and macro-dimensions. Understanding the structure-property relationship of materials, especially in the nano-dimension, is necessary for proper drug design and development of organic semiconducting materials. In this context, cocrystals provide a means to modulate the physico-chemical properties of organic solids. For example, the modulation of the mechanical properties is important in the pharmaceutical industry for improving the tabletability. The mechanical properties may be affected by packing arrangement, interaction strength and type, and atomic and chemical composition. Herein, we report the influence of alkane and alkene functional groups on the mechanical properties of organic solids based on salicylic acid (SA). The approach affords both isostructural and polymorphic solids. The isostructural alkane functional solid exhibits a two-fold larger Young’s modulus (YM) compared to the cocrystal with the alkene, where the YM refers to the stiffness of the material. Here, the higher YM values are attributed to the presence of a bifurcated weak C-H···O interactions involving the alkane and neighboring SA molecules. On the other hand, in the case of alkene polymorphisms, molecular packing with column arrangement shows higher YM values compared to the herringbone arrangements. Thus, functional groups and crystal arrangements influence the stiffness of the solid organic cocrystals. Moreover, we report the modulation of mechanical properties of salicylic acid (SA) through cocrystallization by variation of propane and butane functionality with bipyridine coformers. We show that the variation of propane and butane functionality in bipyridine coformer with salicylic acid leads to synthesis of cocrystal and salt-cocrystal, respectively. The AFM nanoindentation study revealed that the Young’s modulus values follow the order salicylic acid < cocrystal << salt-cocrystal. The highest Young’s modulus values of the salt-cocrystal, among the studied systems, are attributed to the presence of strong N+–H···O– and O–H···O– interactions. On the other hand, higher Young’s modulus values of the propane-based cocrystal compared to the macro-dimensional salicylic acid are attributed to the stronger O–H ···N hydrogen bonding. Thus, homologous alkane functional groups can influence the mechanical properties of the organic solid crystals. Additionally, in situ solid-solid polymorphic phase transformation and nucleation of a metastable and elusive polymorph of SA cocrystals in combination with 4,4’-bipyridine were studied. Understanding the solid-solid phase transformations and nucleation mechanisms are important for proper control over the parameters associated with the synthesis of targeted crystalline solids with desired crystal structure. Using in situ powder X-ray diffraction (PXRD) and terahertz time domain spectroscopy (THz-TDS) data we showed that the Form II polymorph transforms to Form I over time. AFM imaging and nanoindentation techniques were utilized to follow and quantify in real-time the solid-solid polymorphic transformation of the metastable Form II to the thermodynamically stable Form I on a single crystal basis. AFM in situ single crystal data revealed that the metastable Form II has a rod-shaped morphology and relatively high elasticity (Young’s modulus), which transforms to prism-shaped nanocrystals of much smaller sizes with significantly reduced elasticity. The AFM imaging reveals that the single crystals on the order of 80-150 nm to undergo catastrophic changes in morphology that are consistent with cracking and popping owing to a release of mechanical stress during the transformation. The nucleation mechanism for the polymorphic transformation is not spatially localized and occurs over the entire crystal surface. The higher mechanical properties of the metastable Form II is due to the presence of the additional interlayer C-H···O interactions. Furthermore, we have studied the electrical properties of boron-based cocrystals. More specifically, cocrystallization of a nonconductive 2,4-difluorophenylboronic ester catechol adduct of a 4,4’-bipyridine (BEA) host with two aromatic semiconducting guests (pyrene and tetrathiafulvalene) generated conductive cocrystals with variable charge carrier mobilities. Charge carrier mobilities of the cocrystals with either pyrene or tetrathiafulvalene were measured using conducting probe AFM (CP-AFM). The incorporation of π-rich aromatic guests through face-to-face and edge-to-face π-contacts results in electrically conductive cocrystals. The cocrystal with tetrathiafulvalene as a guest shows approximately 7 times higher charge carrier mobility than the cocrystal with pyrene. Overall, the current dissertation demonstrates the AFM-based method development and applications towards materials characterization to measure the morphological, electrical, mechanical, and phase-states at both nano- and macro-dimensions. The high spatial precision of the methods developed enables us to better understand the controlling factors for materials design and processing across nano- and macro-dimensions.