A medical device includes a polymer scaffold crimped to a catheter having an expansion balloon. The scaffold is crimped to the balloon by a process that includes heating the scaffold to a temperature below the polymer's glass transition temperature to improve scaffold retention without adversely affecting the mechanical characteristics of the scaffold when later deployed to support a body lumen. Additionally, before crimping begins the scaffold is placed on a support by an alignment carriage and deionized to remove any static charge buildup on the scaffold before placing the scaffold within the crimping mechanism.