A group company can use HMRC's online filing software unless they have to report any group transactions (for example Group Relief). You must report group transactions on the supplementary page CT600C and this is not included in the HMRC software. You can of course use commercially available software to submit your return online.
No matter what software you use, you must set up an HMRC Corporation Tax online account before you can submit returns online.
Guidance for groups of companies setting up online accounts can be found on the Groups of companies: what to consider before setting up your online account page.