bottom of the filter goes into the box about 3 centimeters so that the mesh wire part is above the box. Remember that you want the filterd air to go outside into your room not back into te box. The inline fan fits directly to the bottom of the box INSIDE the box itself. It is pushing air up through the filter. You can use a 4 inch inline if you want too. You could also use a 5 or 6 inch inline. Just make sure that you have the proper reducer and the needed room to attach it to the bottom of the filter. The model show originally has a 4 inch bottom. Mine has a 6 inch bottom. it all depends on the size of the inline fan you own.