We report a technique for the alignment of self-assembled protein systems, such as F-actin bundles and microtubules, in a surface-modified titanium or silicon microfluidic device. Assembling filamentous protein systems in a confined geometry produces highly aligned samples for structural and mechanical studies. Biomolecular self-assembly can be investigated in a controlled fashion under different molecular concentration gradients and conditions along a channel length. We have shown that surface-modified devices produced via a high aspect ratio etch process in titanium and silicon can be used to confine and control such macromolecular assemblies and present examples of F-actin bundles and microtubules in this system.