Being a difficult-to-cut material, Fiber Metal Laminates (FML) often pose challenges during conventional drilling and require judicious selection of machining parameters to ensure defect-free laminates that can serve reliably during their service lifetime. Helical milling is a promising technique for producing good-quality holes and is preferred over conventional drilling. The paper compares conventional drilling with the helical milling technique for producing holes in carbon fiber-reinforced aluminum laminates. The effect of machining parameters, such as cutting speed and axial feed, on the magnitude of cutting force and the machining temperature during conventional drilling as well as helical milling is studied. It was observed that the thrust force produced during machining reduces considerably during helical milling in comparison to conventional drilling at a constant axial feed rate. The highest machining temperature recorded for helical milling was much lower in comparison to the highest machining temperature measured during conventional drilling. The machining temperatures recorded during helical milling were well below the glass transition temperature of the epoxy used in carbon fiber prepreg, hence protecting the prepreg from thermal degradation during the hole-making process. The surface roughness of the holes produced by both techniques is measured, and the surface morphology of the drilled holes is analyzed using a scanning electron microscope. The surface roughness of the helical-milled holes was lower than that for holes produced by conventional drilling. Scanning electron microscope images provided insights into the interaction of the hole surface with the chips during the chip evacuation stage under different speeds and feed rates. The microhardness of the aluminum layers increased after processing holes using drilling and helical milling operations. The axial feed/axial pitch had minimal influence on the microhardness increase in comparison to the cutting speed.