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I want to filter my beer then put it in the bottles for the second fermentation (aka making the beer fizz). I am worried that I will get rid of all the yeast and end up with flat beer.

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You are right to be worried, assuming the filtration you intend is of sufficient size to remove yeast, of course. Options would be to not filter, or maybe force-carbonate in a keg, then fill bottles from the keg. –  jsled Jan 17 '11 at 17:59
    
is it posable to secondary ferment in a carboy to get rid of some of the cloudiness, then have a third fermentation in the bottles to make it fizzy? –  Twizzle Jan 17 '11 at 20:20
    
Yes, you can either do a secondary fermentation in a carboy, or just leave it in your primary for a few more weeks. After it's bottled and carbonated you can cold-crash it, which will get your beer nice and clear (this can take at least a few weeks after bottling). –  Room3 Jan 18 '11 at 13:30
    
Question needs to be reformulated to explain what 2nd fermentation actually is vs carbonation, as well as some of the other good points mentioned here. Downvoted. –  TinCoyote Jan 19 '11 at 19:15
    
What is the reason you are wanting to filter? For taste or clarity? –  Bullet86 Jan 19 '11 at 22:02

3 Answers 3

If you filter out all the yeast then there won't be any yeast to eat your priming sugar and carbonate in the bottle. Though in actuality I would imagine filtering all of the yeast out of your beer is a difficult feat.

If you bottle condition, the yeast in the bottle is going to multiply and create a sediment on the bottom of the bottle. If you are careful with your bottles, you can pour carefully to avoid letting most of this sediment into your glass.

But if you want to have absolutely no yeast in your bottle then you are going to have to find some other way of carbonating your beer (eg: force carbing via keg).

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If you are a homebrewer, I would recommend avoiding any sort of filtration when bottling or kegging until you're a very advanced brewer. You will need to force carbonate if you filter.

If you are simply trying to get rid of some of the cloudiness, make sure you use a yeast that is not low flocculation (medium is ideal, because highly flocculant yeast might need to be roused if conditions aren't good).

You can indeed transfer your beer to a secondary fermentation vessel (i.e. another carboy) and age it for a while for additional clarity. You can also leave your beer to settle in the bottling bucket for 30-90 minutes after transferring from your fermentor to allow everything to settle.

Ultimately, I rarely worry about clarity in my beer. If it tastes good, it's a successful beer. That said, I usually end up with clear beer because I do most of what I suggested, though I tend not to rack to secondary anymore and instead let my primary fermentation go for 3-4 weeks (you're not going to get any off flavors from yeast in that time, but it will clear up some).

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Since you're primarily looking for clarity in your beer, then the easiest solution is to cold-crash it.

Cold-crashing basically consists of:

  1. Moving the beer (and not the trub) to another vessel (anything you'd use for a secondary)
  2. Placing the beer in the fridge for ~2 days to allow the beer to settle out
  3. Bottling as usual

The cold temp will really help clarify the beer. It doesn't harm the beer or affect the flavor at all, and there's still plenty of healthy yeast in the beer to handle bottle conditioning.

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