macOS Markup – How to Copy an Image from Screenshot’s Markup

The Icon\r file is used when you're about to change folder's icon: when you change the icon, it is not actually applied to the folder itself but rather to the Icon\r file inside the folder in question.

You can remove the file via terminal with rm $'Icon\r'

Alternatively, if you want to delete the file through Finder, you must make it visible first; also something you can do via terminal: SetFile -a v $'Icon\r'

Somewhat related info on how to change file's or folder's icon via Terminal: Changing a file or folder icon using the Terminal

… And be sure to see Icon? file on OS X desktop on Super User.

I use this AppleScript:

tell application (path to frontmost application as text)
    set f to POSIX file (path of document 1) as text
    close document 1
end tell
tell application "Finder" to move f to trash

A hackier version that works with a few more applications:

try
    tell document 1 of application (path to frontmost application as text)
        set f to path
        close
    end tell
on error
    tell application "System Events" to tell (process 1 whose frontmost is true)
        value of attribute "AXDocument" of window 1
        set f to do shell script "x=" & quoted form of result & ";x=${x/#file:\\/\\/};x=${x/#localhost/};printf ${x//%/\\\\x}"
        keystroke "w" using command down
    end tell
end try
POSIX file f
tell application "Finder" to move result to trash