Colloidal crystals with non-close-packed structures, such as body-centered cubic (bcc) structures, are of high interest. Nanosized protrusions, prepared from colloidal crystals, are interesting for biomimetic applications. Herein, self-assembly approaches for synthesizing colloidal crystals with square lattice nanoprotrusions are presented. In the first approach, spin-coating and subsequent heating of colloidal silica and acrylic monomer results in a bcc-like arrangement; the number of stacked colloid layers and the colloid density of these compounds are important in the formation of this structure.Moreover, prolonged heating exposes colloids from acrylic monomer, with square lattice nanoprotrusions formed. In the second approach, the protrusions are fabricated in a shorter time by replacing some of the acrylic monomer with volatile media. Only certain volatile media, such as a solvent with a structure similar to diethylene glycol, exhibit the formation of square lattice protrusions. These bottom-up approaches contribute toward high-throughput techniques for fabricating metastable square lattice colloidal arrangements.