The trees - a 70-year-old sequoia and oak - in Balclutha's Christie St reserve have been at the centre of a dispute between Balclutha resident Maxine Evans and the council.
Legal costs over the matter had ballooned out to $40,000 for the council.
The High Court declined Ms Evan's claim for an injunction and judicial review in December.
Ms Evans confirmed she is required to pay $11,929.
Last year, the council decided to remove the sequoia and oak trees following safety concerns raised by neighbouring residents.
Ms Evans sought an injunction to stop the trees being felled and a judicial review, having previously "expressed her disappointment at the council's decision".
The sequoia and oak trees are 30m and 18m high respectively, and were planted in the 1950s.
The High Court report said if the council was successful in proceedings, it would normally be entitled to costs.
Ms Evans said the wording and definition as to what constituted an amenity tree remained unclear.
"What puzzles me is reading the council's register of significant trees in the district, there are only two trees mentioned as having amenity status," she said.
A sequoia tree at Tapanui Cemetery and another at Waihola Domain were cited as the only amenity trees, Ms Evans said.
She confirmed she was planning an appeal.
"There are several things we feel are not right."
