A fast protocol for prototyping hydrophobic disposable poly(alkyl methacrylate-co-methyl methacrylate) copolymer sample support arrays for matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) of proteins by atmospheric molding is introduced. The sample support arrays were replicated by molding prepolymer alkyl methacrylate solutions into sandwich molds containing a micromachined silicon master, an aluminum spacer, and glass cover plates, followed by UV-initiated in situ polymerization under atmospheric pressure. The fabrication procedure enables a simultaneous fabrication/modification of single-use polymer arrays by a targeted selection of functional groups of the copolymerized monomers during molding. The one-step modification during the fabrication is demonstrated for enhanced protein adsorption to the modified materials by introduction of hydrophobic butyl-, dodecyl-, and octadecyl groups to the polymer backbone without a need for additional surface coating or derivatization. The MALDI-MS performance of the new polymer chips was tested for spectral measurements of bovine pancreas insulin, horse heart myoglobin, and bovine serum albumin. The protein adsorption to the new hydrophobic copolymer chips was studied for bovine pancreas trypsinogen; the sample desalting parameters, such as time and volume, were optimized for myoglobin as model proteins. A significant signal increase was achieved after efficient desalting of an insect Delta11-desaturase membrane protein fragment from a complex elution buffer (100 mM phosphate, 10 mM tris(hydroxyethyl)aminomethane, 0.5 M NaCl, and 10 mM ethylenediamine tetraacetic acid) on the poly(butyl methacrylate-co-methyl methacrylate) copolymer chip (monomer ratio 8:2 v/v) by simply washing the target zones. The new chips offer reduced sample manipulation and device fabrication times as well as simple operation.