In Meshmixer, operations generally are applied to the selected object. If you just have one Mesh in the scene, then you don't need to worry about it. But if you have two or more objects, then you have to make sure you have the right one selected. You can change the selected object(s) by left-clicking. Hold shift while left-clicking to multi-select/de-select. When an object is not selected, it is drawn in a darker shade of grey, as shown in the image below-left.
Left: Sphere object is selected and visible. Right: Sphere object is selected and invisible.
You can also hide objects in the scene. When an object is hidden, you cannot select it by clicking in the scene, although you can select it using the object browser (see below). To hide (or show) the selected object, use the Ctrl/Cmd+V hotkey. If there are many hidden objects and you would like to show them all, you can quickly do that using the Ctrl/Cmd+Shift+V combo.