This was a sci-fi exploration novel that I read about 10 years ago.
A few humans land on a deserted alien world that is technologically more advanced. They do not know what happened to the original inhabitants but they go exploring to find out.
They explore using the advanced transportation system with clear "bubbles" that they would step into and it travel through underground tunnels to anywhere in just a few minutes.
There are other alien creatures on the planet; none have visible eyes but they can still see.
The original inhabitants had trapped themselves in their machine they built. They are still on the planet but as "ghosts" and can only talk to each other and observe what the humans are doing.
The woman who came with them dies at the end and one of the guys gets depressed because he loved her and enters the strange machine where he finds the inhabitants and directs them to the exit to leave the machine.
Then they bring the woman back to life.