The easiest way would be to create a list such as 
 
ftp://user:pass@host[:port]/path/file1.ext 
ftp://user:pass@host[:port]/path/file2.ext 
ftp://user:pass@host[:port]/path/file3.ext 
 
Change the local file browser to the desired download location and then turn on the clipboard monitor and copy the links, FlashFXP will add them to the download queue. 
 
FlashFXP can handle multiple ftp:// links 
 
If this wont work or you need another way to do it perhaps you can be more specific about what you're trying to do.
		 
		
		
		
		
		
		
		
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