Either flash chromatography with C18 silica or prep HPLC should easily remove any metal salts from an organic compound.  

If these organic molecules is not soluble in water solvent. You can use water( ultra pure) to remove metals and then you can filtrate your compounds. 

Yours is a million dollar question :-). Reducing the levels of a number of different metals, in a highly polar compound, to ppb level will be very difficult. Can you share more information about the structure of your compound? maybe the functional groups present in the molecule?

If your compound is neutral or negatively charged, you could pass a solution through a cation exchange resin, or CM-Sephadex, in H+ form.  Use methanol-water to ensure that the resin beads remain hydrated and permeable.

To get to ppb levels, a high-purity analytical grade resin might be required.

@Matthew R Mills, Yes I know the chromatographic method is the suitable one. But it is not practicable for me as my organization has a metric ton level production of this molecule.  @Jacek Martynow, it is actually 1,1,1(tris hydroxyphenyl)ethane, THPE. with three -OH groups it is highly polar and readily soluble in methanol. @James Demers, is this molecule is possible to pass through the ion exchange resin?

The usual resins are polystyrene based, so you might see some retention of a triphenyl species if the solvent contains too much water.  Polyacrylate resins might solve such a problem.

Thanks James, is it possible to do for a large amount of samples. I never used the resin for this purpose. Could you please provide a brief process?

Ion exchange resins are used on large scale for water purification, and to remove chloride from caustic in the chlor-alkali process.  In general, the literature on deionization of water should translate well to your methanol solution; conceivably, you could use a resin cartridge intended for water deionization.  The big variable is how much water is needed in the methanol to ensure permeability and ion exchange functionality.  Pure methanol might cause the beads to shrink, leading to channeling or collapse of a column that was initially packed with water.  To the extent that you can use water as solvent, this complication will be mimimized.

In practice, one simply slurries the resin into a column and lets it settle with gravity flow of the solvent.  You can then rely on gravity flow for your product solution, or you can pump it through.  I'd start with a mixed-bed resin (H+ and OH- resins), perhaps 5% water in methanol as solvent. I'd avoid significant changes in solvent composition once the column is packed.  You'll have to experiment with water content and flow rates.  Resin quality (and cost) may be a factor - I don't know the rates at which ppb metals might leach out of the commercial resins.  Commercial deionizers can produce >16 MOhm water, which has only ppb ion concentrations (mostly bicarbonate from atmospheric CO2).

Mixed bed resins are difficult to regenerate, so if economics call for re-use of the resin, you might switch to separate cation and anion columns in series. 

EDTA MAY HELP

Thanks for your valuable suggestions and guidance...

adding EDTA to the mixture can help!, check this paper about soil purification

B Sun, F.J Zhao, E Lombi, S.P McGrath, Leaching of heavy metals from contaminated soils using EDTA, Environmental Pollution, Volume 113, Issue 2, July 2001, Pages 111-120, ISSN 0269-7491, http://dx.doi.org/10.1016/S0269-7491(00)00176-7.

Usually materials as silica (silicon dioxide) or aluminiumoxide often used in flash chromatography may adsorb these metal traces. I propose adding small portion to a sample solution in methanol and checking the AAS from time to time. This is simple and may give an idea of up-scaling this procedure using a column or filter cartridge.

How I can remove metals like Li+ and Na+ from Organic solution