Disclosed are systems and methods for mechanically reducing an amount of the skull material in a finished, molded part formed from amorphous alloy using an injection molding system. Skull material of molten amorphous alloy can be captured in a trap before molding such material. A cavity can be provided in the injection molding system to trap the skull material. For example, the cavity can be provided in the mold, the tip of the plunger rod, or in the transfer sleeve. Alternatively, mixing of molten amorphous alloy can be induced so that skull material is reduced before molding. A plunger and/or its tip can be used to induce mixing (e.g., systematic movement of plunger rod, or a shape of its tip). By minimizing the amount of skull material in the finished, molded part, the quality of the part is increased.