Keepmark let you encrypt files using GPG/PGP algorithms. Currently supported is only symetric encryption (password protected). With Keepmark you can encrypt and decrypt files, or display preview of the file.
With Keepmark encryption i very easy - use context menu, select right command and enter password:
When you want to access to encrypted files - put password to preview panel or decrypt it via resource context menu.
When you don't have access to Keepmark you can always decrypt your files using command line GPG tool:
gpg --decrypt --output path/to/output.md path/to/input.md.gpg