Your methodology is perhaps the most essential part of your research. You cannot possibly complete research without a research methodology which clearly delineates how you are performing research. If you are not certain, you should consider discussing with your advisor and researching common methodologies in your field.
In some fields, the question and field inherently define a certain methodology. For example, in anthropology there are well established procedures for examining new artifacts. So defining your methodology may not be much challenge.
In other fields, you may need to determine the model, theory, or framework you think suits your problem before you can seriously think about the methodology. For example, in meteorologic investigations, once you've picked a modeling program you want to use it will often define the data collection and input that you will use.
If you do not know where to start, consider looking through some research method books in your field and learning more about measurement in your field.
Make sure that in your literature review you research, read up on, and thoroughly discuss the methodology that you use! You must demonstrate that you have a good understanding of your methodology (as well as any associated theories, models, measures, or tools that you use).