Flower seed threshing and cleaning are challenging because many flowers have tiny seed, e.g., the 1000-seed weight of Begonia is 0.01 g, and others have odd-shaped seed, e.g., Tagetes has pappus-bearing seed and Fibigia has winged seed. There is a lack of information on the threshing and cleaning of flower seeds. At the Ornamental Plant Germplasm Center, a small-plot grain belt thresher was modified by disengaging its winnower and a special chute installed to collect the threshed seed and chaff together for cleaning. A custom-made threshing board is used for small samples. The seed with chaff is passed through screen with mesh size that allows all the seed to pass through so that the big pieces of chaff are retained and separated, i.e., scalping. Accurate selection of the next scalping screen (SS) is critical so that the mesh size is just right for at least 95% of the seed to pass through to remove all the chaff larger than the seed. The seed is then sieved on a grading screen (GS) of mesh size that retains at least 95% of the seed to remove all the chaff smaller than the seed. A seed blower is used to further separate the remaining chaff and empty seed based on weight and surface area by adjusting the blowing velocity (BV). A vibratory separator (VS) is used for species with round seed, e.g., Antirrhinum. An X-ray machine is used to monitor the cleaning process. The SC, GS, BV, and VT are given for Agastache, Anisodontea, Antirrhinum, Aquilegia, Aster, Astilboides, Begonia, Belamcanda, Bergenia, Cleome, Coreopsis, Dianthus, Eupatorium, Gaillardia, Geranium, Gypsophila, Iris, Lilium, Lysimachia, Myosotis, Nothoscordom, Oenothera, Passiflora, Penstemon, Petunia, Platycodon, Ranunculus, Rudbeckia, Silene, Stokesia, Synnotia, Tagetes, Talinum, Thalictrum, Verbena, Veronica, and Zinnia.