This thesis focuses on the interdisciplinary biophysical research field, in which physical approaches are applied to study the biological phenomena. Specifically, the main object of the research in this thesis is to target biological species,especially the amyloid fibrils by using Atomic Force Microscope (AFM) and several relevant technologies. In the main section, we firstly present the high-resolution AFM and AFM-IR measurement on the LHCII on the chloroplast lipid membrane, and investigation on the regulation of the xanthophyll pigments, including violaxanthin and zeaxanthin, on the supramolecular organization and structural conformation of LHCIIs on the chloroplast lipid. Then, the novel vis-PTIR technique shows it capability for ultra-sensitive nanoscale imaging and chemical analysis.This AFM-based approach is enhanced by both the gap plasmon and the instrumentation resonance that shows a high-spatial resolution and single-molecule layer sensitivity. Then, my following researches are focused on the protein aggregation and amyloid fibrils that are associated with various neurodegenerative diseases. The first research target is to investigate the environmental factors on protein aggregation kinetics and amyloid formation. We designed the experimental setup to highlight the influence of sedimentation, microgravity, hydrodynamic flow,air-water interface on the protein aggregation kinetics and distinct microscopic steps of aggregation.The results show that the interface promotes the primary nucleation and hydrodynamics enhances the secondary nucleation, whereas the sedimentation and microgravity contribute no significant impact on the aggregation kinetics. Similarly, to understand the polymorphism phenomenon encountered in the preceding research, we performed an additional experiment with well-controlled environmental kinetics. This environmental kinetics originated from the different combinations of hydrodynamics and interface. This experiment proves that the amyloid polymorphism is under the control of environmental kinetics, as well as the order-order transition among the polymorphs. This conclusion is expected to expand our understanding on fibrillization mechanism and also to show its significance in the biomaterial applications. Last, but not the least, we propose another possible mechanism of amyloid aggregation, hierarchically assembly model(HAM), that enables the protofilament intertwining to form higher-ordered mature fibrils. In this experiment, this novel intertwining model based on statistical result of AFM images, is verified with the modelling and multiple experimental evidences, that may enrich our current knowledge of fibrillization mechanism and mature fibril formation.In the end of this thesis, we briefly summarize the presented scientific works and their potential in the applications. In addition, we developed the perspective of these research in the future with several examples of the interesting topics.