The root of a fillet weld is the intersection of the two joining parts. A fillet weld must penetrate to the root as a minimum but it doesn't have to go beyond that. Many times, the weld will be deeper than the root but that is considered incidental and usually is not evaluated. If you should want penetration to go past the root then you could specify a groove weld of some type, either partial or complete penetration, with a fillet weld "reinforcement".
Hope this helps,
CHGuilford
There is a great article in "THE AMERICAN WELDER", page 13 regarding Metal Cored Electrode Basis. We produce seamless flux cored wires and based on your base metal and the mechanical values requirements I would be pleased to provide you with a sample for evaluation in your process. Please provide more info about your steel, joint config. etc.