Metal assisted chemical etching with interconnected catalyst structures has been used to create a wide array of organized nanostructures. However, when patterned catalysts are not interconnected, but are isolated instead, vertical etching to form controlled features is difficult. A systematic study of the mechanism and catalyst stability of metal assisted chemical etching (MACE) of Si in HF and H₂O₂ using Au catalysts has been carried out. The effects of the etchants on the stability of Au catalysts were examined in detail. The role of excess electronic holes as a result of MACE was investigated via pit formation as a function of catalyst proximity and H₂O₂ concentration. We show that a suppression of excess holes can be achieved by either adding NaCl to or increasing the HF concentration of the etching solution. We demonstrate that an electric field can direct most of the excess holes to the back of the Si wafer and thus reduce pit formation at the surface of Si between the Au catalysts. The effect of hydrogen bubbles, generated as a consequence of MACE, on the stability of Au catalysts has also been investigated. We define a regime of etch chemistry and catalyst spacing for which catalyst stability and vertical etching can be achieved.