Added multiline regex flag.

Regex replace.py

import clipboard, console, re

mytext = clipboard.get()

# User input text
matchedText = console.input_alert("Find", "Enter text/regex to find.")
replacedText = console.input_alert("Replace", "Enter text to replace.")

# Regex find and replace
mytext = re.sub(matchedText, replacedText, mytext, flags=re.MULTILINE)

# Displays new text; comment out if you don't care
# Mostly useful for testing
console.clear()
print mytext

# Sends new text back to clipboard for pasting
clipboard.set(mytext)