I recently got rid of a nasty trojan on Windows and want to migrate to Linux(Ubuntu). I want to run a Live CD so that I can format an SD card to put my brand new firmware on my router and format the HDD so I can install Ubuntu. In this case, is it possible to get my system infected or to infect the SD card? I mention the fact that my Windows 7 is a genuine license and also my nod32 but I do not trust the fact that my virus is gone.
If the virus only infected Windows, then you won't be infected if you don't run anything from this instance of Windows. So booting from a Linux CD is fine, and your computer will be fine if you install Linux (or even if you reinstall Windows from scratch).
If you accessed the SD card from windows, the virus could try to copy itself to it and then spread to other machines. The other machines would have to be vulnerable to the virus, which in practice pretty much means they'd have to run Windows. Reformat the SD card under Linux if you're worried it might now hold the virus.
In theory a virus could infect some firmware in your computer (the BIOS, or any other firmware). However firmware-infecting malware is extremely rare in the wild. Unless you're concerned that this is a concerted attack from a highly-motivated attacker, rather than some common infect-the-least-protected trojan, don't worry about this.
Windows tends to change very slowly, and gives the chance to virus/trojan authors to target very specific bugs on Windows' binaries or binaries from third party applications.
The way GNU/Linux distributions are made makes it especially difficult for viruses to exploit vulnerabilities (when available).
As stated by Gilles, you can be safe by formatting your SD card from within the Linux Live CD.