Membrane-based separation processes such as nanofiltration and reverse osmosis are increasingly used for water purification. In several applications, chlorine and other oxidizing agents must be removed from the feedwater, as it can degrade the polyamide-based selective layer of these membranes. However, operating without biocidal agents increases the risk of biofouling, a phenomenon in which microorganisms such as bacteria, algae, and fungi adhere to and proliferate on membrane surfaces and modules, forming a biofilm. The biofilm can clog membrane surface and module channels, reducing performance in terms of permeate flow rate and quality. Managing biofouling requires frequent system cleaning and maintenance, which increases operational costs and may shorten membrane lifespan. To address this challenge, various strategies have been investigated to either prevent biofilm formation or enhance cleaning efficacy. These include enzymatic or chemical cleaning protocols, as well as emerging methods involving physical techniques such as magnetic fields and sonication. An essential step in assessing the effectiveness of these treatments is the qualitative techniques and structural visualization of the membrane surface. Scanning electron microscopy (SEM) is widely used for this purpose, enabling high-resolution imaging of biofilm or residual fouling. This chapter details the procedures that must be performed for sample preparation to ensure accurate SEM visualization of membrane biofouling. Key steps such as fixation, dehydration, and drying are outlined as well with practical tips to preserve the structural integrity of biofilm.