Is there a way to block someone from popping up on your chat? or seeing when you are on-line?

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Yes. You need to create a list first. Go to Friends, then click the Create A List link at the top of the page. Call it your Block list. Add in any of your friends that you no longer wish to speak with via chat. Then, log into Chat and click the green Go Offline button that appears next to the Block list grouping. Everyone else, except the people on the Block list, will see you online.