Quick Definition: Limiting scientific study to natural causes
From Rational Wiki:
Methodological naturalism is the label for the required assumption of philosophical naturalism when working with the scientific method. Methodological naturalists limit their scientific research to the study of natural causes, because any attempts to define causal relationships with the supernatural are never fruitful, and result in the creation of scientific “dead ends” and God of the gaps-type hypotheses. To avoid these traps scientists assume that all causes are empirical and naturalistic; which means they can be measured, quantified and studied methodically.
However, this assumption of naturalism need not extend beyond an assumption of methodology. This is what separates methodological naturalism from philosophical naturalism – the former is merely a tool and makes no truth claim; while the latter makes the philosophical – essentially atheistic – claim that only natural causes exist.