A method for fabricating chemical gradients on planar and nonplanar substrates using grayscale lithography is reported. Compliant grayscale amplitude masks are fabricated using a vacuum‐assisted microfluidic filling protocol that employs dilutions of a carbon‐black‐containing polydimethylsiloxane emulsion (bPDMS) within traditional clear PDMS (cPDMS) to create planar, fully self‐supporting mask elements. The mask is then placed over a surface functionalized with a hydrophobic coumarin‐based photocleavable monolayer, which exposes a polar group upon irradiation. The mask serves to modulate the intensity of incident UV light, thereby controlling the density of molecules cleaved. The resulting molecular‐level grayscale patterns are characterized by condensation microscopy and imaging mode time‐of‐flight secondary‐ion mass spectrometry (ToF‐SIMS). Due to the inherent flexibility of this technique, the photofuse as well as the gradient patterns can be designed for a wide range of applications; in this paper two proof‐of‐concept demonstrations are shown. The first utilizes the ability to control the resulting contact angle of the surface for the fabrication of a passive pressure‐sensitive microfluidic gating system. The second is a model surface modification process that utilizes the functional groups deprotected during the photocleavage to pattern the deposition of moieties with complementary chemistry. The spatial layout, resolution, and concentration of these covalently linked molecules follow the gradient pattern created by the grayscale mask during exposure. The programmable chemical gradient fabrication scheme presented in this work allows explicit engineering of both surface properties that dictate nonspecific interactions (surface energy, charge, etc.) and functional chemistry necessary for covalent bonding.