How to remove embossing from leather
Disclaimer: I've not tried this, so I can't guarantee it will work.

One thing that I've seen suggested is to soak the leather with water and then heat it - this should cause the fibres to swell and reduce the depth of the debossing (embossing is raising a material, debossing is lowering it).

The issue with this is that I've only heard of it being done on untreated veg-tanned leather, which your shoes almost certainly are not.

In order to successfully have the leather absorb the water, you'll first need to remove the covering. This can be done with a little soap and water, or (more drastically, and more likely to damage your shoes) with acetone or rubbing alcohol. 

Once you've done that, stuff your shoes with something to keep their shape, and then soak + heat (a hairdryer or heat gun is the best option here).