diff --git a/src/neuron_proofreader/merge_proofreading/merge_inference.py b/src/neuron_proofreader/merge_proofreading/merge_inference.py
index b2f67ad4..de26515f 100644
--- a/src/neuron_proofreader/merge_proofreading/merge_inference.py
+++ b/src/neuron_proofreader/merge_proofreading/merge_inference.py
@@ -198,6 +198,7 @@ def __call__(self):
         t0 = time()
         self.log("Search Graph...")
         merge_sites = self.search()
+        self.graph.remove_merge_sites(merge_sites)
 
         # Report results
         t, unit = util.time_writer(time() - t0)