I have created a site for my orginisation but i used a downloaded copywrited software to create it. When i created it i did not know that it was haram to download copywrited softwares. My question is can i keep the website and modify it with a free program or so i need to remove all the files and start over?
It is not permissible to use tricks to download or copy programs and discs whose authors have not given permission to download them or copy them for free. That is because copyright is recognized. This has been discussed previously in several answers, including the following: no. 95173, no. 72848, no. 102352. We have explained that this is a general principle, but there may be exceptions to that in some cases:
1 – If it is not available in the marketplace; in that case it is permissible to copy it for personal use or charitable distribution, and it is not to be sold or profited from.
2 – If there is a great need for it and the owners are demanding more for it than it is worth, and they have already made enough money to cover their costs with a reasonable amount of profit, and that is something to be decided by experts. In that case it is permissible to copy it for personal use, not with the aim of selling it.
3 – If these disks belong to a company in a state that is at war against the Muslims, there is nothing wrong with copying them, because those whose rights are to be respected are: Muslims, non-Muslims living under Muslim rule, and non-Muslims with whom the Muslims have a peace treaty – not non-Muslims who are in a state of war against the Muslims.
Based on that, if what you used comes under the heading of one of these exceptions, then there is no blame on you.
If that is not the case, then you have to ask Allah for forgiveness and repent, and contact the authors of the program and ask for their forgiveness. If they insist on the price of the program, then look at the original copy and pay its price, and keep your website.
And Allah knows best.