Cell culture is a scientific method for explaining biological processes that allows data on safety and efficacy to be obtained with fewer ethical and commercial constraints. The most well-known approach, 2D cell culture, has been in use since the early 1900s. This procedure entails the nourishment and growth of cell cultures on the bottom of a petri dish, flask, or other flat surface. Most cells exist in complex three-dimensional structures composed of multiple cell types within an extracellular matrix. Interactions between cells and between cells and the extracellular matrix all have a significant effect on their behavior. 3D cell culture is a culture environment that enables cells to grow and interact with the extracellular framework in three dimensions. Organoids are three-dimensional multicellular in vitro tissue constructs that mimic their corresponding in vivo organs in such a way that they can be used to study specific aspects of the organ in the tissue culture dish. Because three-dimensional cell cultures and organoids are more physiologically relevant and more closely mimic in vivo tissue, they are gaining popularity. There are numerous examples of photochemical reactions induced by light occurring in biological systems. Photobiomodulation (PBM) stimulates cellular processes by using non-ionizing light sources. Chromophores within a cell interact with these photons, initiating biological cascades that result in a variety of effects depending on the wavelength and fluency used. Photodynamic therapy (PDT) is a type of phototherapy that combines light and a photosensitive drug to induce cell death. Additionally, the photosensitizer can be used as a fluorescent agent to identify cells in which the drug has been localized. These forms of phototherapy can be developed using various cell culture methods to aid in the understanding of disease mechanisms and drug screening, where it is critical to optimize and validate protocols for the specific model system.