You will always have a bit of yeast in the bottom of the bottles with bottle conditioned beer. There are commercial breweries where you'll notice it too! I know Rogue, especially their Shakesphere Stout, has a dusting of yeast on the bottom. (You can keep that yeast, and save it, but that's for another post!)
There are a couple of things to do to minimize the amount of yeast in the bottles. One is a long enough primary. I am NOT a fan of the "month long primary" that seems to be preached around here lately, but certainly that won't hurt the beer. I think 2-3 weeks is plenty of time.
A couple of keys, though- first, use a flocculant yeast like S04. That will compact down to a very tight yeast cake, especially if you can chill the fermenter before transferring to the bottling bucket.
Two, careful siphoning will really help. I start siphoning in the middle of the fermenter and lower it as the level of the beer drops. I avoid the trub at the bottom.
If you can crash cool (stick the fermenter in the fridge, for example) for a day or two before bottling that will help suspended solids drop out of suspension.
It sort of goes without saying, but don't bottle a beer until it's clear. Because when it does clear, you'd have the stuff drop out in the fermenter, rather than the bottle!
Lastly, when you serve the beer, chill it a couple of days in the fridge and don't move it around. When you pour it, open it and pour it in one pour and leave the last 1/4" of beer in the bottle. That way the sediment stays in the bottle and doesn't get poured into your glass. I think Revvy has a "how to pour a homebrew" guide that is really helpful for friends who aren't accustomed to homebrew.