I suggest reading the skinning documentation. It basicly works like this.
Most skin designers use HTML to create their skins, then zip their HTML files to create a skin package. When the skin packag ei uploaded it is parsed by DNN and an ascx file is created, which is what DNN Actually uses. If the html file is called mycoolskin.html, DNN will create a file called mycoolskin.ascx.
Within the HTML for each skin there are a number of tokens like [SEARCH], [LOGIN], [USER] [SOLPARTMENU], etc. When DNN parses the HTML file to create .the .ascx file, it puts the appropriate code for a control in place of the token. You need to find the HTML file for the skin you are using (usually in the " /portals/_default/skins/NAMEOFSKINPACKAGE" folder, and remove the text "[SEARCH]".
Some skin designers do not include the HTML file, in which case you will have to remove the Search Contol code from the ascx file (it will be in two places). If you modify the HTML file you need to parse the skin package (In the Skins tab) which will make DNN create new ascx files for the skins.