I want to move my eCommerce site currently running on wordress and woocommerce to a different CMS (Prestashop) The current site only has about 100 pages indexed.My question is can I remove the site from search console and re-add the domain when I'm done with the new site? The current site does not have a lot of traffic as I only added it two months or so ago so. I'm not to worried about loosing traffic.  
Changing to a new CMS - Search Console
google;cms
As you have changed the CMS, one thing I would recommend you do is removing the 'old cms sitemap' replace it with the 'new one'. I also recommend checking that the same version of your website should be submitted into the Search Console. If your website is accessible using http://www.example.com then it should be submitted with 'http' and 'www'.These two things needs to be taken care in Google Search Console once you change website CMS.