There are different sizes of motherboards, which in turn require different cases to house them. Case form factors share the names of the motherboards they support, and some of the common ones include ATX, Micro ATX (mATX), FlexATX and Mini ITX. ATX motherboards are perhaps the most common, and the largest of the four, measuring at most 12" x 9.6" (305mm x 244mm). A Micro ATX board is at most 9.6" x 9.6" (244mm x 244mm), a FlexATX is 9.0" x 7.5" (229mm x 191mm) and a Mini ITX comes in at a tiny 6.7" x 6.7" (170mm x 170mm). ATX and mATX are by far the most popular motherboard sizes for consumer motherboards, and hence, most cases are made to support one or both of these sizes.
I maybe be misreading what you are saying. Are you talking about whether a motherboard will WORK with the CPU you have in mind? If it is that, make sure the motherboard support the right socket for the CPU. What CPU is it? Intel or AMD? What model CPU?