I see a frog in your picture.
There is an emblem in the original drawing.
I think that 'in' is the preferred preposition in these instances.
'We have eliminated the emblem' means the act of elimination was done at some time in the past and the result still remains now.
'We eliminated the emblem (we need an adverb phrase to indicate the time in the past.).' means that the act of elimination was done at some time in the past, but we are not telling you whether it was put back or not.