The present invention discloses a method for forming germanides on substrates with exposed germanium and exposed dielectric(s) topography, thereby allowing for variations in the germanide forming process. The method comprises the steps of depositing nickel on a substrate having topography, performing a first thermal step to convert substantially all deposited nickel in regions away from the topography into a germanide, selectively removing the unreacted nickel, and performing a second thermal step to lower the resistance of formed germanide.