Hi Yanhe,
I guess you mean you have no atomic structure fitted inside, only the map?  Zones are defined using atomic coordinates.

However, without any atoms, you can interactively  (manually by moving a sphere with the mouse or trackpad) delete parts of the map using the Volume Eraser tool, see:

<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/voleraser.html>

It is in the menu, Tools... Volume Data... Volume Eraser.

Another possible approach is to try segmenting the map, e.g. menu: Tools... Volume Data... Segger. 
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/segger/segment.html>

This has many features and controls to group/ungroup segmentation regions, etc., but if you can get the bilayer segmented separately from the protein density, then you can select (Ctrl-click) and hide the regions you don't want to see (Segger menu:  Regions... Hide) 

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On May 17, 2021, at 1:00 PM, Yanhe Zhao <yanhezhao1990@gmail.com> wrote:
>
> To whom may concern,
>
> This is Yanhe Zhao, from UT Southwestern Medical Center.
>
> I was curious that how can I exclude the lipid bilayer to show the transmembrane protein electron density when "zone" could not be used as I have no sequence and pdb information.
> Thanks a lot in advance for any input.
>
> Best regards,
> Yanhe