How to get flannel material the same size?

I'm trying to make a rag quilt. I cut my squares the same size ( 6 in by 6 in) using a template. The material I'm using is flannel so as you know, it tends to expand and contract at a lot different rates than regular cotton or most other materials. What I want to know, is even though I used a 6"x6" template my squares are different sizes. Before piecing my squares together, how can i make sure they are the same size?