We ran into this problem here today and I figured out why its happening and a solution. The problem has nothing to do with what renderer you are using, and is still a problem in the most current version of Maya, as of this writing: Maya 2018 update 2.
Maya obviously has two render layer systems, the old (legacy) system, and the newer renderSetup layers. If you are using the renderSetup layer system (which I believe Maya defaults to nowadays) when you create a renderSetup layer, it also creates a corresponding legacy layer. Since two objects cannot have the same name in Maya (unless they are parented to different things) the legacy layer is named with rs_ at the start of the name.
UNFORTUNATELY, when you use the <RenderLayer> preset in the Common tab of Render Settings, it grabs the name of the LEGACY layer (with the rs_ at the start),not the renderSetup layer, even if you are using renderSetup layers. I have no clue what 'genius' at Autodesk implemented the renderSetup system and then forgot to support it in Render Settings, but I digress....
Ok, so whats the solution? I am using Maya's PreRender and PostRender mel scripts to get around the problem. When you render, a PreRender script switches around the names of both the legacy and renderSetup layers. After the render is kicked off, a PostRender script renames everything back to how it used to be. Your renders will come out fine and not have the annoying rs_ in the file or folder names. This solution will work on any version of Maya, and for any renderer. It is harmless to use even if somebody at Autodesk bothers to fix the bug properly (gasp).
1) Save this code as PreRender.py in your Maya prefs scripts directory
in linux its /home/ (USER NAME)/maya/ (VERSION NUMBER)/prefs/scripts.
In Windows its C:\Users\ (USER NAME) \ My Documents\maya\prefs\scripts
def PreRender():
import maya.cmds as mc
### To not conflict with the renderSetup layers, the auto-generated old layers start with rs_
### Unfortuantely the Maya Common 'File name prefix' <RenderLayer> setting uses the OLD layer system names,
### despite rendering from the new layer system. So the layers are all named rs_. This snippet renames
### the renderSetup layers to rl_(layer name) and renames the rs_(layer name) layers to just (layer name).
### a corresponding postrender script names them back.
for Layer in mc.ls(typ="renderSetupLayer"):
if not Layer.startswith("rl_"):
try:
mc.rename(Layer,"rl_"+Layer)
except:
pass
for Layer in mc.ls(typ="renderLayer"):
if Layer.startswith("rs_"):
try:
mc.rename(Layer,Layer[3:])
except:
pass
2) Save this code to the same directory, using the name PostRender.py
def PostRender():
#### renames the layers back to what they were before rendering, restoring the original renderSetup name and adding rs_ back to the old system render layer names
import maya.cmds as mc
for Layer in mc.ls(typ="renderLayer"):
if not Layer.startswith("rs_"):
try:
mc.rename(Layer, "rs_" + Layer)
except:
pass
for Layer in mc.ls(typ="renderSetupLayer"):
if Layer.startswith("rl_"):
try:
mc.rename(Layer,Layer[3:])
except:
pass
3) Every time you make a new scene you want to render, go to the Common tab of Render Settings, and add this to pre Render Mel under the Render Options rollout.
python("from PreRender import *;import PreRender;PreRender.PreRender()");4) Add this to the post Render Mel under the same rollout.
python("from PostRender import *;import PostRender;PostRender.PostRender()");
