A method of fabricating a cross-layer pattern in a layered object is disclosed. The method is executed by an additive manufacturing system and comprises: dispensing a patterning material onto a receiving medium to form a first pattern element; dispensing a first layer of modeling material onto the first pattern element while forming a first open cavity exposing at least a portion of the first pattern element beneath the first layer; and dispensing patterning material onto the exposed portion of the first pattern element and the first layer to form a second pattern element contacting the first pattern element.