Machining of poly(methyl methacrylate) (PMMA) by laser has been extensively studied in engineering research for several applications including microfluidic manufacturing and rapid prototyping. However, very few investigations have taken into consideration the wide range of physico-chemical characteristics of commercially available PMMA that can often affect the quality of the laser-machined structures. These characteristics are often ignored, with many manufacturing publications focusing on a single source of PMMA. To understand the different bonding strengths and laser-cut qualities in the context of our ultra-fast prototyping technique, four types of PMMA have been examined. Molecular weights, and thermal properties have been determined and their roles on the bonding strength and CO2 laser cut quality, including kerf width and taper angle, have been investigated. This study demonstrates that the choice of material, for rapid prototyping of multi-layered structures via CO2 laser machining and solvent-assisted bonding, is crucial and provides a practical guide to researchers selecting PMMA material for use in micro-engineering and microfluidic rapid-prototyping.