Can you filter beer while siphoning into the bottles? If we can't how is filtering normally done?

Filtering requires pressure to push the beer through a set of filter pads. Pressure can be achieved using CO2 to push the beer from one keg through a filter and into the next keg, or with the use of a diaphragm pump to push beer through a set of filter pads (though the later arrangement poses serious risks of oxidation for the homebrewer without CO2 on hand.) In a commercial brewery either of the above methods may be used. The sediment on the bottom is yeast, highly nutritious and a benefit in the aging process of higher alcohol beers (plus 8% ABV for instance.) Most homebrewers decant their beer out of the bottle and into the glass in a single pour to leave the yeast behind in the bottle.

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