I am currently playing an imperial pysker in a rogue trader game and have just got this large full suit of xeno armor. At the same time i also just unlocked Shape Flesh. So my question is how does armor and Shape Flesh work? Guessing from the name alone it only shapes flesh, so if i were in guard flak or storm trooper carapace would the power not work or would it shape around the armor.

Over all I know it is up to my GM. But I like to think things through.

There is an argument to be made either way.

As a GM I would tend to say no, it won't work on armor.

As a player I would make the argument for precedent of the warp being capable of manipulating the armor also. -- See Chaos Marines

So the only way to unlock the full potential of the power you have to wear little to no armor?

For mechanical purposes the shape flesh's natural armor bonus does stack with worn armor. I guess it would be up to your GM to descide the form and function of the "grown" armor if its suppose to be large natural plates or what in which case in a roleplaying sense it could hinder you from using certain inflexible armors or such.

This goes for most of the effects of shape flesh as far as I understand

Thread necromancy, but slightly justified.

According to the Black Crusade errata, natural armor (like from Shape Flesh or the Machine Trait) stacks with worn armor. However, it probably should be left up to your GM.