The scientist should look at various morphological features of the plant. He should begin with broad features; such as type of roots and venation. If fibrous roots are present then the plant may belong to monocotyledonous. In case of tap root, the plant may belong to dicotyledonous. This can be further confirmed with the presence of parallel or reticulate venation and number of cotyledons in the seeds. 
 
After that, the scientist should look at the type of phyllotaxy, inflorescence, etc. Which will help in classifying the plant in order and family. If it is a flowering plant, then a detail study of various floral parts can give various clues about a particular family or order. Type of placentation can be studied by looking at the arrangement of seeds inside the fruits.  Finally, arrangement of antheridium and gynoecium can help the scientist to confirm a particular family for the new species. The scientist also needs to rule out exact similarity with any other existing species before arriving at a unique name for the new species found.