So the building I am Modeling has different layouts for each floor. Some Buildings have the same overall shape but different layout inside. Others are smaller in overall shape. I am using the surface matching tool to intersect the entire model and then matching entire model. Everything gets matched except for a few spots of the in between floors where it thinks the bottom floor ceilings are outside bound and the top floors are ground bound. What am I doing wrong and how can I fix this.

So the building I am Modeling has different layouts for each floor. Some Buildings have the same overall shape but different layout inside. Others are smaller in overall shape. I am using the surface matching tool to intersect the entire model and then matching entire model. Everything gets matched except for a few spots of the in between floors where it thinks the bottom floor ceilings are outside bound and the top floors are ground bound. What am I doing wrong and how can I fix this.bound.