We report a strategy for rapidly generating arbitrary microscale patterns of biomaterials that can be used to create complex surface gradients or sequentially assembled into functional three-dimensional microarchitectures. In this approach, mask objects and transparency-based masks are used to direct multiphoton photocrosslinking (MPP) of proteins. Unlike conventional methods for controlling direct-write multiphoton fabrication, 1 this simple graphical-based approach allows new patterns to be created within minutes, enabling rapid iteration and optimization of experimental parameters. We demonstrate use of this strategy to transfer detailed shapes (e.g., the silhouette of a house fly) into biomaterial patterns and to fabricate microchambers capable of trapping and incubating a single motile bacterium.Multiphoton lithography provides high-resolution microfabrication capabilities in three dimensions, using nonlinear excitation to promote photopolymerization 2 or protein photocrosslinking 3,4 within a femtoliter voxel created by tightly focusing a pulsed laser beam. By scanning the fabrication voxel through reagent solution, complex three-dimensional microscale objects 1,5 have been produced with lateral feature sizes as small as ∼120 nm using synthetic materials 1 and ∼250 nm using proteins. 4 Figure 1A demonstrates our approach for mask-directed multiphoton lithography. Here, light from a femtosecond titanium: sapphire (76 kHz) laser is sent through an unmodified confocal scan box to raster the beam in a rectangular pattern at a focal plane positioned between the scan box and an inverted microscope. This focal plane (mask plane) is conjugate with the front focal plane of the microscope objective. By placing an object (such as Musca domestica, Figure 1A) or a pattern printed on transparency film within the mask plane, microstructures representing the object silhouette or mask negative can be fabricated at the objective focal plane. Fabrication objects, created by multiphoton crosslinking of bovine serum albumin (BSA) or other proteins, display feature sizes of F mask /M obj , where F mask is the feature size in the mask and M obj is the magnification of the objective/lens system. Minimum achievable feature sizes are determined by the spatial confinement of multiphoton absorption and the diffusion distances of reactive intermediates. 6 From a practical standpoint, masks printed on standard low-resolution transparencies (1200 dpi) can be used with a conventional 100X (1.3 NA) objective to produce features of ∼0.5 µm ( Figure 1A-C)sa scale appropriate for addressing a broad range of applications in cell biology and microtransport. 7 Using this general approach, multiple masks can be used in concert to fabricate complex patterns containing gradients of crosslinked protein ( Figure 1B). Here, a negative transparency photomask was placed in the mask plane to define the microstructure shape and a second fully opaque mask was translated during scanning at a constant velocity to vary the integrated laser exposure across th...