Methods and systems for hydroprocessing heavy oil feedstocks to form an upgraded material involve the use of a colloidal or molecular catalyst dispersed within a heavy oil feedstock, a hydrocracking reactor, and a hot separator. The method can include selectively implanting an impurity into a underlying layer containing silicon using a mask to form a boron-added region and an etched region. The first regions are disposed in the substrate and surrounded by the annular well region.