You could write a quick bash script using SCP/SFTP for transfers and if you are using say OpenSSL:

crypt-send.sh

#!/bin/bash
openssl des3 -salt -in file1.txt -out file1.crypt -pass pass:CHANGEME
openssl des3 -salt -in file2.txt -out file2.crypt -pass pass:CHANGEME
# This is the SCP Option
scp <file to upload> <username>@<hostname>:<destination path>
scp <file to upload> <username>@<hostname>:<destination path>
# This is the SFTP Option (Make Batch File)
sftp -b files.list username@hostname

If you want to use SFTP or SCP setup keys, but if you need to do SFTP option too use the batch option just put this into a files.list file with this script:

cd some-path/
binary
put file1.crypt
put file2.crypt
quit

See if that helps!