This protocol describes the implementation of laser scanning lithography (LSL) for the fabrication of multifaceted, patterned surfaces and for image-guided patterning. This photothermal-based patterning technique allows for selective removal of desired regions of an alkanethiol self-assembled monolayer on a metal film through raster scanning a focused 532 nm laser using a commercially available laser scanning confocal microscope. Unlike traditional photolithography methods, this technique does not require the use of a physical master and instead utilizes digital "virtual masks" that can be modified "on the fly" allowing for quick pattern modifications. The process to create multifaceted, micropatterned surfaces, surfaces that display pattern arrays of multiple biomolecules with each molecule confined to its own array, is described in detail. The generation of pattern configurations from user-chosen images, image-guided LSL is also described. This protocol outlines LSL in four basic sections. The first section details substrate preparation and includes cleaning of glass coverslips, metal deposition, and alkanethiol functionalization. The second section describes two ways to define pattern configurations, the first through manual input of pattern coordinates and dimensions using Zeiss AIM software and the second via image-guided pattern generation using a custom-written MATLAB script. The third section describes the details of the patterning procedure and postpatterning functionalization with an alkanethiol, protein, and both, and the fourth section covers cell seeding and culture. We end with a general discussion concerning the pitfalls of LSL and present potential improvements that can be made to the technique.