Simplest way to password protect a directory and its contents without having to create new files?

I would like to password protect or encrypt a directory and all the files within it (for the whole directory tree below it). I do not want to bother the whole home directory, I want a specific directory with some files and folders in it. I would like to be able to encrypt the directory or decrypt it using a password. Command line would be nicest to use. I don’t want to have to create a new file as an encrypted version and then, delete the previous ones which are the non-encrypted version.

How can I encrypt a file?

I would like to download some files from my server into my laptop, and the thing is that I want this communication to be as stealth and secure as it can be. So, far I came up using VPN, in that way I redirect the whole internet traffic of my laptop via my server. Additionally, I tried to send a file using ftp and observing Wireshark at the same time. The communication seems to be encrypted, however I would like also to encrypt the file itself (as a 2nd step security or something like that).