Hi Tania,
Unfortunately, you can't filter the Milestones by Portfolio Item on the Timeline. They will still be displayed based on their date. You can uncheck the "Show Workspace Scoped Milestones" to hide the milestones that are scoped to the entire workspace. You can also filter the items being displayed to specific milestones. You can do this through the filter option built into the page. I don't think either of these options is exactly what you are looking for though, and I'm sorry that I couldn't find one that better meets your needs.