I’ll self-answer. I went through steps and it’s straight forward. Pycharms (the IDE I’m use) automatically found the new libraries too. Here are the steps I followed to remove the extra Python libraries on Mavericks that were not native to it and not installed by brew.
Step 1:
The native Python 2.7.x version lives here /System/Library/Frameworks/Python.framework/Versions/2.7 (or 2.6, etc), so you can remove any Python that got installed elsewhere.
sudo rm -rf /System/Library/Frameworks/Python.framework/
Or, according to this article, you should brew install both python 2.7 and python 3.x,
and avoid using system python in Mavericks.
Step 2:
Remove python in Applications directory (the one where all your apps are).
cd into folder /Applications and ls | grep Python to see what have.
Then remove:
sudo rm -rf "Python 3.3"
Step 3:
>>> brew prune
sample output:
Pruned 0 dead formula Pruned 46 symbolic links from /usr/local
Step 4: Run steps recommended by brew doctor
sudo brew link python3
Sample output
Linking /usr/local/Cellar/python3/3.4.0… 19 symlinks created