Using the NppExec plugin, you can grab the selected text and pass it through another program, and then grab the results. Here is one where I had NppExec grab the entire contents of the given window, save it to a temporary file, pass it through gpg to decrypt it, and paste the contents back into that same NPP window.

cls
npp_save
cmd.exe /c exit %RANDOM%														// cannot access $(SYS.RANDOM) directly through NppExec, but can tell cmd.exe to return it as a value
set tempfile = $(SYS.TEMP)\NppGpgFile_$(EXITCODE).tmp							// create random tempfile name
set ascfile = $(SYS.TEMP)\NppGpgFile_$(EXITCODE).asc							// create associated ascfile name
sci_sendmsg SCI_SELECTALL														// select all
sel_saveto $(ascfile) :a														// save selection to the ascfile	(use :a to save as ansi, to prevent unicode prefix ÿþ getting embedded)
gpg.exe --output "$(tempfile)" --decrypt "$(ascfile)"							// decrypt
sel_loadfrom $(tempfile)														// replace selection with results
sci_sendmsg SCI_DOCUMENTSTART													// deselect
rm -rf "$(tempfile)" "$(ascfile)"												// cleanup temp files
npp_save

Since you want to make use of what you’ve already selected, you wouldn’t need (for eample) the sci_sendmsg SCI_SELECTALL, because you would want to leave the selection alone. So, based on your description that it’s already selected, here’s something that should give you a starting place:

cmd.exe /c exit %RANDOM%														// cannot access $(SYS.RANDOM) directly through NppExec, but can tell cmd.exe to return it as a value
set destfile = $(SYS.TEMP)\NppFilterDestinatino_$(EXITCODE).tmp					// create random destfile name
set sourcefile = $(SYS.TEMP)\NppFilterSource_$(EXITCODE).tmp					// create associated sourcefile name
sel_saveto "$(sourcefile)" :a													// save selection to the sourcefile	(use :a to save as ansi, to prevent unicode prefix ÿþ getting embedded)
c:\path\to\program.exe --output "$(destfile)" --source "$(sourcefile)"			// this is the program you're filtering it through; this will work if your program can take input and output filenames at the command prompt
// however, if your program only uses STDIN and STDOUT, then do something like:
// type "$(sourcefile)" | c:\path\to\program.exe > "$(destfile)"				// this uses windows pipes and redirection so your program.exe takes STDIN and outputs to STDOUT, but NppExec can interface with the files
sel_loadfrom "$(destfile)"														// replace selection with results
rm -rf "$(destfile)" "$(sourcefile)"											// cleanup temp files

I left in the random file naming for the tempfiles, because it should keep collisions from occurring. I included options for either command-line arguments to your program.exe, or using windows type, along with an input pipe and output redirection, so that your program could use STDIN->STDOUT.

NppExec comes with pretty thorough documentation, but if you have any questions about this outline, feel free to ask.