Agarose hydrogels of varied elastic modulus can be patterned into 100-mu m-wide channels with wall heights of 60 mu m. After modifying the hydrogels with chloroacetic acid (acid gels), they are amenable to modification with amine-containing ligands using EDC-NHS chemistry. Using both rheometry and atomic force microscopy (AFM) nanoindentation measurements, the elastic modulus of unmodified hydrogels increases linearly from 3.6 +/- 0.5 kPa to 45.2 +/- 5.5 kPa for 0.5 to 2.0 wt/vol % hydrogel, respectively. The elastic modulus of acid gels is 2.2 +/-0.3 kPa to 16.2 +/- 1.6 kPa for 0.5 to 2.0wt/vol %, respectively. No further changes were measured after further modifying the acid gels with fibronectin. Confocal images of rhodamine-modified acid gels show that the optimal filling viscosity of the agarose solutions is between 1 and 4 cP. This new method of patterning allows for the creation of substrates that take advantage of both micron-scale patterns and variably elastic hydrogels.