I wish to a add a couple config lines to all the routers and switches in the network. Instead of longing into each device, can we do this at once using any script or tool? Please note that we require an user name and an RSA(a time varying password) token to login into any of these devices.
What you want to do is pretty straight forward and there are plenty of good options out there to update the config on multiple devices.
However in your situation this is complicated by having to use a multi factor one time password.
If you have a method that allows you to download and upload the config of each device without logging in to each via SSH, perhaps SNMP and tftp/scp then you could download all the config, run a script over the files to update, then load them back in again. You would be having to do your own scripting to make that go through.
Longer term I would consider setting up an NMS Linux host with MFA login and pre shared keys for SSH to run these kind of scripted config changes.