Biopsies are not perfect, because they are only checking a small number of cells from a large area. If they do identify cancer, they are accurate 90% of the time.
However, if they fail to see cancer the rate of false negatives can be as high as 40%. It is common that 30% of biopsies result with data that is inconclusive.
Surgery
Surgery is not commonly used for benign nodules. This is unless they are large enough to cause significant pain or impingement on the muscles, nerves, or blood vessels of the throat.
Radio Ablation
This is a non-surgical option for those with nodules large enough to cause local problems but lacking in signs suggesting they may be cancerous (and therefore do not warrant excision).
In a recent, large study, radio ablation has been shown to reduce nodule volume by a substantial percentage (typically 60 to 80%).
It has also been shown not to alter thyroid function. Those who had normal thyroid function before ablation retained it afterward.2