The second sentence is correct = I'm not sure if we can do this. We use if, in this context, when expressing a feeling of uncertainty or lack of confidence on a particular matter. The first sentence is not really correct. People do say this sometimes but it is not good English. You can say, however, I am sure that we can do this.

Except for the duplicated "we" in the second sentence, both sentences are correct and common. There is no difference between "to not be sure that/if/whether ..." Additionally, "to doubt that/if/whether ..." is similar but stronger. To be polite, many people say "I am not sure that ..." when they mean "I doubt that ..." I'm not sure that ... I'm not sure that our supplier will deliver on time. I'm not sure that the government can solve the problem. I'm not sure that she told the truth. I'm not sure if ... I'm not sure if our supplier will deliver on time. I'm not sure if the government can solve the problem. I'm not sure if she told the truth. I'm not sure whether ... I'm not sure whether our supplier will deliver on time. I'm not sure whether the government can solve the problem. I'm not sure whether she told the truth. I doubt that ... I doubt that our supplier will deliver on time. I doubt that the government can solve the problem. I doubt that she told the truth.