The disclosed computer-implemented method for remediating the effects of malware may include (1) identifying a file on a client device, (2) determining, using a digital fingerprint that identifies the file, that the file's reputation is unknown, (3) in response to determining that the file's reputation is unknown, logging changes made by the file to the client device, (4) determining that the changes made by the file are to be reversed, and (5) in response to determining that the changes made by the file are to be reversed, instructing the client device to reverse the changes made by the file to the client device. Various other methods, systems, and computer-readable media are also disclosed.