A modem only transmits the data, the computer uses a protocol to connect to the ISP. Different types of protocol exist, but I think you're probably thinking of FTP - File Transfer Protocol.
If the modem is used to connect to an ISP for an internet connection, than the standard internet protocols and utilities can be used for file transfer. They include ftp, sftp, http and the wget command. If the modem is used to establish a serial connection such as a terminal emulation session, protocols like kermit and xmodem/ymodem/zmodem should be available that perform errorfree file transfers.