When you press Ctrl-C over a file in the file manager, the file's contents IS NOT copied to the clipboard. A simple test: select a file in file manager, press Ctrl-C, open a text editor, press Ctrl-V. The result is not file's contents but its full path.

In reality the situation is a bit more complicated because you can't do the opposite - copy a list of filenames from a text editor and paste them into file manager.

To copy some data from command line to X11 clipboard you can use xclip command, which can be installed with

sudo apt-get install xclip

to copy contents of a file or output of some command to clipboard use

cat ./myfile.txt|xclip -i

the text can be then pasted somewhere using middle mouse button (this is called "primary selection buffer").

If you want to copy data to the "clipboard" selection, so it can be pasted into an application with Ctrl-V, you can do

cat ./myfile.txt|xclip -i -selection clipboard

To be able to copy files from the command line and paste them in a file manager, you need to specify a correct "target atom" so the file manager recognizes the data in the clipboard, and also provide the data in correct format - luckily, in case of copying files in a file manager it's just a list of absolute filenames, each on a new line, something which is easy to generate using find command:

find ${PWD} -name "*.pdf"| xclip -i -selection clipboard -t text/uri-list

(at least this works for me in KDE). Now you can wrap into a small script which you can call, say, cb:

#!/bin/sh

xclip -i -selection clipboard -t text/uri-list

then you put it in ~/bin, set executable bit on it and use it like this:

find ${PWD} -name "*.txt"| cb

Nice, isn't it?