Yes absolutely.
You can send shell commands via raw commands (Ctrl+R) or you can toggle the RAW Command Line (Main menu > View > RAW command line) and access it directly via the main window.
By default FlashFXP will accept any non-defined command as a SSH command (with a warning prompt) but you can also prefix the commands with
/shell
You can also create custom commands so that the command can be executed with a shortcut key or without having to type it in each time.
For example you can use something like this
Extract tar archive
When the command executes the %f token is replaced with the name of the selected item in the file list.
If you have multiple items selected then the entire command will execute for each item selected.
Additional information and more examples can be found in our help file and in this forum.