I have few categories with custom URL. Basically I am using these categories to launch filter navigation pages from the menu. Is it recommnended to use both noindex/nofollow or just noindex? I am running magento 1.9.1
If I understand your question correctly, you are referring to internal links.
As per Matt Cutts: "for internal links, links within your site, I would try to leave the nofollow off."
This is because you want to let the rank flow with your links. But he also makes a point that if it really is a useless page, like a login, then it doesn't hurt you to use nofollow, although there is no reason for it. I wouldn't use it.