What you do is configure a crypt pointing at a local directory, and copy your encrypted files into there with the same directory structure.
Something like this
$ rclone config
n) New remote
d) Delete remote
s) Set configuration password
q) Quit config
e/n/d/s/q> n
name> localcrypt
Type of storage to configure.
Choose a number from below, or type in your own value
1 / Amazon Drive
\ "amazon cloud drive"
2 / Amazon S3 (also Dreamhost, Ceph, Minio)
\ "s3"
3 / Backblaze B2
\ "b2"
4 / Dropbox
\ "dropbox"
5 / Encrypt/Decrypt a remote
\ "crypt"
6 / Google Cloud Storage (this is not Google Drive)
\ "google cloud storage"
7 / Google Drive
\ "drive"
8 / Hubic
\ "hubic"
9 / Local Disk
\ "local"
10 / Microsoft OneDrive
\ "onedrive"
11 / Openstack Swift (Rackspace Cloud Files, Memset Memstore, OVH)
\ "swift"
12 / Yandex Disk
\ "yandex"
Storage> 5
Remote to encrypt/decrypt.
Normally should contain a ':' and a path, eg "myremote:path/to/dir",
"myremote:bucket" or maybe "myremote:" (not recommended).
remote> /tmp/encrypted_files_go_here
How to encrypt the filenames.
Choose a number from below, or type in your own value
1 / Don't encrypt the file names. Adds a ".bin" extension only.
\ "off"
2 / Encrypt the filenames see the docs for the details.
\ "standard"
filename_encryption> 2
Password or pass phrase for encryption.
y) Yes type in my own password
g) Generate random password
y/g> y
Enter the password:
password:
Confirm the password:
password:
Password or pass phrase for salt. Optional but recommended.
Should be different to the previous password.
y) Yes type in my own password
g) Generate random password
n) No leave this optional password blank
y/g/n> y
Enter the password:
password:
Confirm the password:
password:
Remote config
--------------------
[localcrypt]
remote = /tmp/encrypted_files_go_here
filename_encryption = standard
password = *** ENCRYPTED ***
password2 = *** ENCRYPTED ***
--------------------
y) Yes this is OK
e) Edit this remote
d) Delete this remote
y/e/d> y
e) Edit existing remote
n) New remote
d) Delete remote
s) Set configuration password
q) Quit config
e/n/d/s/q> q
$ mkdir /tmp/encrypted_files_go_here
$ rclone ls localcrypt: