A 3x3 subwindow structure in MATLAB refers to a layout for displaying multiple plots within a single figure, specifically arranged in three rows and three columns, totaling nine graphs. The confusion often arises from interpreting the term as a coordinate system rather than a plotting arrangement. The subplot function in MATLAB is commonly used to create this structure. Users can efficiently visualize multiple datasets simultaneously using this method. Understanding this layout enhances the ability to present complex data clearly.