Follow the instructions in your literature procedure.
For an aqueous workup of most organic compounds this will involve:
Diluting the reaction mixture with a solvent for workup
(this is the organic layer). Exceptions
Washing the Organic Layer with various aqueous solutions.
Some of the byproducts generated during the reaction will be neutralized
or removed by dissolving in the aqueous layer.
Ideally, the two layers will be clearly visible.
If the result is one cloudy layer, you have an emulsion.
Drying the Organic Layer with one of the drying agents.
Filtering off the drying agent.
Rotoevaporation to remove the solvent.
The residue left is the crude product, ready for diagnosis.
Certain types of compounds are more difficult to isolate than
others--if your product might be volatile, soluble in water,
charged at low or high pH (e.g. an amine or a carboxylic acid),
unstable, or possesses stench, see
How to Handle.