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I have two raster files in ArcGIS 10.1, raster 1 and raster 2 all with values and similar spatial resolutions, and overlay in some areas.

I want to replace values in raster 1 with those in raster 2 where there is an overlay.

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If you want to use raster calculator, try this:

Con(IsNull(raster1),raster2, raster1)

meaning that if raster1 has no value, it will use the value of raster2, otherwise it will use the value of raster1. Under the Enviroments... tab you can select your desired extent of the output raster. This will only work, if your raster1 has a lot of gaps.

However, I guess the best solution would be to use the mosaic to new raster tool in your Data Management toolbox, since you only want to replace values and not perform any other operation. Look at the following example: mosaicraster

Make sure the Mosaic operator is set to your raster2, so that values from it will be used instead of raster1.

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