Different layers in different Master Pages

Hi Marco:

I'm a visual learner, so I almost always answer with a picture or a short video clip. My take on this initial confusion to your question was the reference to layers versus frames on a layer. In my pic below, there is one layer with four rectangle frames on that one layer. 

It's very common to have multiple parent pages (previously called master pages) in a single InDesign file. And an efficient way of working is to base a new parent page on a previous parent page. When you do that, everything from the first parent page is visible on the new one. You can Ctrl+Sh+click (Mac: Cmd+Sh+click) on any frame to select and delete it. Here's my clip to provide the visual: the A Parent has the four frames—two blue and two pink—and both are visible on the B Parent, which is linked to the A Parent. I am Cmd+Sh+clicking the pink frames and pressing Delete, and then assigning B Parent to body pages 2–3.

~Barb

We often hear this question from seasoned users of Photoshop, where layers work very differently. Perhaps you'd get useful information by telling us what you're trying to do? For instance, it sounds to me like you want to make a second parent page based on the first, and then selectively remove content from the second page only. This is doable - but not with layers. 

Here's a long thread where many people try to explain this concept (layers vs. page objects) until someone finally got it.

A layer in InDesign exists on all pages and spreads of the document.. This includes Parent (Master) pages.

You don't have to put page objects on each page using a particular layer, but the layers are there, nonetheless.

It's just the way InDesign works.

Layers are document-wide. You can't remove a layer from specific page only (if I understand your question correctly).