Panel Data Structure with Fixed Effects Model

I need to estimate linear fixed effects model with 1 dependent variable and 2 independent variables and I'm wondering how I should order my data and how I could estimate my model. Currently my data is organized in excel in 3 different datasheets with column headers for the companies and row headers for the years. Resulting in a N*T matrix for all my variables. Do I need to reorder my data to a NT * 1 matrix for my dependent variable and a NT * 2 (2 independent variables)? Or is there an easier way to estimate a fixed effects model in matlab?