AppleScript: How to close notification alerts from a specific application?
I tested the following example AppleScript code under macOS 10.12.5, and it closed the Alerts style messages from Calendar.

tell application "System Events"
    tell process "NotificationCenter"
        set windowCount to count windows
        repeat with i from windowCount to 1 by -1
            if description of image 2 of window i is "Calendar" then
                click button "Close" of window i
            end if
        end repeat
    end tell
end tell


Note: This is example AppleScript code which contains no error handling. Add appropriate error handling as needed, required and or wanted.