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The only way I can think of to do this is to keg the beer first, and then use a counter-pressure-bottle filler to fill the bottles. As long as you aged the keg a bit first to allow it to clear, this should provide relatively clean bottles of beer.
You can't do this with natural bottle carbonation as far as I know because it will always leave sediment.
Its very hard to get zero sediment. Probably the best overall method would be to keg the beer, and then filter it while driving it into a counter pressure bottle filler. The in-line filtering and counter-pressure filler combo should leave no sediment as long as the beer was properly aged first.