Maybe try a Aggregator + BoundingBoxReplacer (3D) after your excel coordinates. What you have will fail to clip because you can’t clip with points.

Or you have it around the wrong way and your IFC model needs to be the clipper.

Here are possible 2 scenarios , in one example i am able to clip and in another it fails.

PASS

FAIL 

With Fail i have tried to use IFC model and intersect with Excel coordinates and its work well. ….! It only here in FME that its not clipping :(

Are the features entering the clipper areas? This can be checked by using a GeometryFilter. Do the areas have an area? Can test this usingt the AreaCalculator. Are the areas correct? The GeometryValidator can check this.

If you check the rejected features, what is the fme_error saying?

Anyting in the log?

Are the features entering the clipper areas? yes the Clipper is an Area (3D Room)

This can be checked by using a GeometryFilter. Do the areas have an area? Yes it does have an area. 

Can test this usingt the AreaCalculator. Are the areas correct? Yes it does have area 

The GeometryValidator can check this.

If you check the rejected features, what is the fme_error saying? The rejected feature are okie . No problem with that its the ‘Outside’ ….all those 594 feature (XYZ coordiantes ) are inside the 3D Room and i have check using Navisworks and AutoCad Civit 3D , by overlaying each other. 

Is your issue that all features are outside?

Are the coordinate systems the same? What CRS have the Excel points? CoordinateSystemSetter.

Are the units the same? Designs can be created in millimeters.

The issue is that all the features are outside, that’s correct.

I agree with you @nielsgerrits its now something do do with Coordinates that both items are in. Now i may need help or guidance how to get it all right.

this is now i have checked 

the 3D Cube is ad below

This below 676 point inside the 3D cube

this is topic that i never got it right or understood, Coordinate Setting, here are some basic question 

1. How to know in which coordinate system features are ? 
2. If there is no coordinate system set, how to get both feature into correct coordinate system ?

If you remove the coordinate system in both streams (CoordinateSystemRemover) it might be enough to get it to work.

I’m no expert in this topic so hard to write something that makes sense and be sure it is correct. Reverse engineering a coordinate system is hard. I usually just try what I think it is and if it does not align, it’s not correct.

If you open the 2 streams in one inspector, you can validate this (does one set lies on top of the other, as expected) just connect the 2 sources to 1 inspector.