Pixen features an interface similar to that of Adobe Photoshop. While common tools such as the pencil, eraser and fill tool are included, Pixen also uses a unique left/right tool system. This system enables the user to assign a different tool to the left and right mouse buttons. This can be used effectively when drawing and erasing. Pixen also features an extensive color palette system and, like many other bitmap-based editors, supports editing images by layers; users can organize parts of an image, name them and hide them. Anti-aliasing is not possible to achieve in Pixen due to its focus on pixel art creation.
Pixen was designed from the ground up with a native Mac OS X look and feel. It therefore features a Cocoa interface and makes extensive use of Cocoa controls and paradigms. From a layout perspective, Pixen's interface resembles other raster graphics editors: it features a tool case and separate windows for the canvas, layers and tools.