While high-resolution microscopic techniques are crucial for studying cellular structures in cell biology, obtaining such images from thick 3D engineered tissues remains challenging. In this review, we explore advancements in fluorescence microscopy, alongside the use of various fluorescent probes and material processing techniques to address these challenges. We navigate through the diverse array of imaging options available in tissue engineering field, from wide field to super-resolution microscopy, so researchers can make more informed decisions based on the specific tissue and cellular structures of interest. Finally, we provide some recent examples of how traditional limitations on obtaining high-resolution images on sub-cellular architecture within 3D tissues have been overcome by combining imaging advancements with innovative tissue engineering approaches.