It's a methodology of observation and emopirical measurement. That means it's only going to work on what can be observed and measured, doesn't it?
WRT the above "IT," are you speaking of methodological materialism or of the scientific method?
Not everything that exists can be directly "observed and measured." For instance, the physical laws themselves. And yet without the physical laws, science would have nothing to do.
I had thought the scientific method was about empirical phenomena; i.e., not simply "material" phenomena. Empirical phenomena are not necessarily completely reducible to or explainable in terms of their material components alone (assuming they have any).
For example, those empirical phenomena known as organic systems in nature have a material basis, but they cannot be completely explained in terms of their observable materiality alone. What cannot be directly observed and measured here is essential to understanding the phenomenon under study. For example, the phenomenon's organizational principles — which are ineluctably non-observable.
Capice?