Beam shaping in scattered and uniform scanned proton beam therapy (PBT) is made commonly by brass apertures. Due to proton interactions, these devices become radioactive and could pose safety issues and radiation hazards. Nearly 2,000 patient-specific devices per year are used at Indiana University Cyclotron Operations (IUCO) and IU Health Proton Therapy Center (IUHPTC); these devices require proper guidelines for disposal. IUCO practice has been to store these apertures for at least 4 mo to allow for safe transfer to recycling contractors. The devices require decay in two staged secure locations, including at least 4 mo in a separate building, at which point half are ready for disposal. At 6 mo, 20–30% of apertures require further storage. This process requires significant space and manpower and should be considered in the design process for new clinical facilities. More widespread adoption of pencil beam or spot scanning nozzles may obviate this issue, as apertures then will no longer be necessary.