Merging layers becomes a routine task for anyone who uses Photoshop often. As with most things in Photoshop CC, you can merge layers in several ways. The most common approach merges all visible layers or flattens an image so you can easily move artwork to another project. If you only want to merge two of several layers, the Merge Down option is a quick approach. Photoshop also offers a way to stamp multiple layers into a new layer, without merging and without affecting the other layers. If you have a clipping mask you want to merge, Photoshop has an option for that too.
Merging Visible Layers
Open your Photoshop project and look at the Layers panel. Each layer with an "Eye" icon is visible and will be included in the merge. Click the "Eye" icon beside any layer you don't want merged. If you want to preserve transparency, for example, hide the "Background" layer.
Click the "Layer" menu and select "Merge Visible" to merge all the visible layers. If all layers are visible, selecting "Flatten Image" also merges them.
Save the file in any format using the "Save As" option under the File menu. Use a different file name so you don't write over the original file. Writing over the original file makes it impossible to retrieve the layers after the file is closed.
Merging Specific Layers
Merge two layers without affecting any other layers using the Merge Down option. Begin by selecting the top layer you want merged in the Layers panel. If it's a vector, like a shape layer, you must first rasterize the layer from the Layer menu. Drag the second layer you want merged so it's directly below the first layer. When you select "Merge Down" from the Layer menu, the two layers become one.
Use a keyboard shortcut to stamp multiple layers into a new single layer. Ctrl-click each layer you want to include in the Layers panel to highlight them. When the layers are selected, press "Ctrl-Alt-E" to stamp them. All the layers are stamped into a new merged layer. The individual layers remain unchanged.
Merge the layers that make a clipping mask using Photoshop's Merge Clipping Mask option. First, click the "Eye" icon beside each layer in the Layers panel to hide all the other layers. Select the mask layer -- the one below the layer being masked -- and then select "Merge Clipping Mask" from the Layer menu.
To make multiple layers easier to manage without merging them, group them in folders. Click the folder-shaped "Create New Group" button at the bottom of the Layers panel and then drag the layers into that folder to group them. You can manage the layers as a group or double-click the folder icon to reveal the individual layers inside it.