Pre-version 3.0.0, all the databases that one mongod hosts have to be in the same dbpath folder which can be set via command arguments using the --dbpath flag or the config file.

You could however run multiple mongods and host them individually? either on different ip/ports.

Version 3.0.0 you can use the --directoryperdb flag within the command arguments or config to set multiple directories per database (See https://docs.mongodb.com/manual/reference/program/mongod/#cmdoption--directoryperdb)

Uses a separate directory to store data for each database. The directories are under the --dbpath directory, and each subdirectory name corresponds to the database name.

When you start mongod.exe you can set the database path with the

mongod.exe --dbpath "path to your folder"

setting.

yes it's possible, run mongod process with --dbpath option