When working on a diagram in Visio the use of layers can be a boon. For example, intrusive shapes can be hidden to free up space to work in and different segments of a flowchart can be colour coded for effect. Here are some basic guidelines for working with layers.
When creating a diagram or drawing in Visio, splitting the overall picture into layers is a useful technique that allows the user to concentrate on a particular part of the project. Here are some tips on how to get started in the use of layers.
First of all you may like to add a couple of buttons to your toolbar for ease of use. Go to Tools, select Customise and in the Categories menu click on View. In the Commands menu scroll down to Layer Properties and drag this onto your toolbar. Now go back to the Categories menu and select Format Shape. Go to Layer Tools and drag this onto your toolbar as well. You will now be able to manipulate your layers with ease.
To get started, pull out a square and a circle on your page (if you want to pull out a perfect square and circle instead of trying to gauge with the eye, hold down the shift key as you pull out the shapes). Click onto an area of blank page so that neither of the shapes is selected and you are now ready to assign names to your layers.
Click on your newly installed Layer Properties button and in the dialog box select New and you will be prompted to enter a name for your layer. For the purposes of this demonstration you should keep it simple and name the shapes square and circle, but sticking to geometrical shapes is not essential - you could just as well call them Itchy and Scratchy if you so wished.
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http://www.microsofttraining.net/article-1371-how-create-layers-in-visio.html