All those left-over line segments suggest that you are simply not working accurately enough.
They are the result of duplicate paths not aligning perfectly.
I tried something similar without a glitch:
Fist I drew a simple hexagon, duplicated it 7 times and Pathfinder (panel) Unite to get a hexagon-thingummy like yours.
Then copy-dragged to make 6 of those (left picture).
Then Pathfinder Unite to combine them – See no unwanted segments.
If you want to trim the result, draw a line (3rd picture) and Object > Path > Divide Objects Below then delete the bit you don’t want (4th picture).
I think that if you work accurately, making use of Snap to Point and Smart Guides, you should have no difficulties.
Some of your paths are disappearing because you are using Pathfinder Shape Modes, and some of the paths are open paths. From your screenshots, I see no reason to be using Pathfinder Shape Modes.
Note that the Tooltips on the Shape Mode buttons state "Add to Shape Area", "Subtract From Shape Area", etc. An open straight path has no shape area. So it disappears.
First, why do you want to make the hexagon shapes a Compound Shape? They don't seem to overlap, so what's your reason for that?
Second, if you are not going to make the merely apparent interlocking hex shapes into closed paths, then you can trim them by:
- Draw just one rectangle around the portion that you want to keep
- Select everything
- Pathfinder Divide (lower left icon)
- Object>Path>Cleanup>Unpainted Objects (to remove the no-fill/no-stroke paths from the resulting Group).
At 1) The overall goal is to create a swatch-pattern that I can fill any object with. If you look at image 1, you'll notice the box that cuts out my hex-compund-pattern are possible to align if copied and pasted next to each other, and I would then be able to create a swatch-pattern with my hex-compound-shape.
At 2) Did not solve my issue, but produced this image instead:
It might be that my individual compound-shapes (created from the 7 hexagons) are not aligning properly. I tried to make them align correctly by turning on smart-guides and snap-to-point and view my separate compound-shapes in the 'outline'-view, but this did not do the trick.
Is there a way to make my hex-compound-shapes align perfectly to avoid 'loosing' and 'gaining' lines in my rectungular compound-shape of the cut-out from the large-hex-compound-shape ?
Thanks. I aligned my compound-shapes with snap-to-point and smart-guides. Do I need anyhting else apart from turn these features on under 'view'?
I swithced to 'outline-view' to make sure my shapes overlapped and aligned correctly. But it might be that I haven't been doing this accurately. Is there a way to be absolutely sure the objects are aligned correctly? The align-tool would usually be a good help, but I had to turn my original hex-compound-shape 30 degrees, to make them match each other and I find it hard to make them align now.
Compound Shapes not required. In this example, Pathfinder palette not used at all:
Example of the kind of simple Pathfinder operation I was talking about to perform the trimming when using only strokes (no fills) in the Pattern artwork, and thereby avoid having to draw the unpainted tile rectangle:
If all you needed to do was to make a pattern, why didn’t you say so at the beginning?
Select Show Center (Attributes panel).
Rotate units by 19.107° so that centres align horizontally and vertically.
Drag a no-fill, no-stroke rectangle between centres and Send to Back.
Select all and drag to Swatches panel.
Now you can fill a shape with the pattern.
Rotate pattern only by minus 19.107° to get it back to its original orientation.
Edit: JET got there first but he’s thinking along the same lines as I am!