A system and method for removing residual glutaraldehyde from a natural polymer scaffold crosslinked with glutaraldehyde is provided. The system includes a cleaning solution comprising carbon dioxide and one or more polar solvents and an environmental chamber that can include and a treatment chamber. The environmental chamber is maintained at a temperature greater than 31.1° C. and the carbon dioxide is maintained at a pressure greater than 7.38 megapascals to form supercritical carbon dioxide. A crosslinked natural polymer scaffold treated via the glutaraldehyde removal system and method can have a glutaraldehyde content of less than about 3 parts per million. A crosslinked natural polymer scaffold cleaning solution comprising supercritical carbon dioxide and one or more polar solvents is also provided.