There are provided a method of processing an amorphous material which is capable of forming surface projections of uniform height in desired positions on the amorphous material, and a magnetic disk substrate using the amorphous material. A predetermined pressure is applied to selected parts of a surface of an amorphous material using fine particles having a hardness higher than that of the amorphous material to form high-density compressed layers, and a surface layer of the amorphous material is removed using a treatment agent that has a different removal capacity in the compressed layers and a remaining uncompressed layer, thus making the compressed layers project out. For example, the treatment agent may be an etching solution having a different etching rate in the compressed layers and the uncompressed layer.