The engineering of nanoscale materials can fundamentally determine the macroscopic device functionalities for modern technologies. Similarly, there is also a hierarchy of length scales in nature that connects full-body biological activities with organ-level behavior, and eventually with molecular structures that are also on the nanometer scale. The design for high-performance and reproducible applications is constantly disturbed by structural heterogeneity such as edges, grain boundaries, and variations in domains and phases. The modified material morphology can lead to unique electronic states that impact the ultrafast dynamics of charge transfer or charge recombination. Structural variations are also ubiquitous in biological systems and they are critical to the functional forms of living systems. The knowledge of the structure-property relationship in both fields is highly demanded to achieve controlled, predictable functionalities of either device engineering or a biological body. In this thesis, we present our approaches to entangling the nanoscale heterogeneous information using a novel technique, photoemission electron microscopy, or PEEM. In particular, we will focus on the study of two-dimensional materials and neurological tissues with several variations of PEEM configurations. Chapter 1 introduces the motivations for this thesis, explains the necessary theory background on photoemission and electron imaging, exemplifies PEEM applications that are closely related to this thesis, and provides a summary of the system of study, including 2D black phosphorus, a perylene diimide (PDI)/MoS2 bilayer heterostructure, and ultra-thin mouse brain sections. Chapter 2 describes the details of the experimental apparatus constructed to realize the research goal. We will cover an ultrafast laser as well as two distinct PEEM systems, and explain the setups for polarization-dependent and time-resolved PEEM experiments. Chapter 3 discusses current progress and challenges for preparing and characterizing mechanically exfoliated 2D materials. Chapter 4 details the study of edge-specific characteristics of 2D black phosphorus using polarization-dependent PEEM. Chapter 5 discusses a time-resolved PEEM study on the nanoscale ultrafast dynamics of PDI/MoS2 bilayer heterostructures. Chapter 6 introduces the applications of PEEM to neuroscience and demonstrates the potential for fast 3D imaging as well as the contrast mechanism of osmium-stained biological tissues. Chapter 7 extends the previous discussion and presents a few ongoing experiments that open the opportunities of PEEM to wider applications.