The instability of isolate catalysts during metal-assisted chemical etching is a major hindrance to achieve high aspect ratio structures in the vertical and directional etching of silicon (Si). In this work, we discussed and showed how isolate catalyst motion can be influenced and controlled by the semiconductor doping type and the oxidant concentration ratio. We propose that the triggering event in deviating isolate catalyst motion is brought about by unequal etch rates across the isolate catalyst. This triggering event is indirectly affected by the oxidant concentration ratio through the etching rates. While the triggering events are stochastic, the doping concentration of silicon offers a good control in minimizing isolate catalyst motion. The doping concentration affects the porosity at the etching front, and this directly affects the van der Waals (vdWs) forces between the metal catalyst and Si during etching. A reduction in the vdWs forces resulted in a lower bending torque that can prevent the straying of the isolate catalyst from its directional etching, in the event of unequal etch rates. The key understandings in isolate catalyst motion derived from this work allowed us to demonstrate the fabrication of large area and uniformly ordered sub-500 nm nanoholes array with an unprecedented high aspect ratio of ∼12.