I am playing around with this as well. I am using a copy of the sample theme at the moment while I am learning how to do this in Copperminer 1.4.9 after upgrading from 1.3.5.
My theme.php has this
// HTML template for template sys_menu buttons
// {HREF_LNK}{HREF_TITLE}{HREF_TGT}{BLOCK_ID}{SPACER}
addbutton($sys_menu_buttons,'{HOME_LNK}','{HOME_TITLE}','{HOME_TGT}','home',$template_sys_menu_spacer);
addbutton($sys_menu_buttons,'{MY_GAL_LNK}','{MY_GAL_TITLE}','{MY_GAL_TGT}','my_gallery',$template_sys_menu_spacer);
addbutton($sys_menu_buttons,'{MEMBERLIST_LNK}','{MEMBERLIST_TITLE}','{MEMBERLIST_TGT}','allow_memberlist',$template_sys_menu_spacer);
addbutton($sys_menu_buttons,'{MY_PROF_LNK}','{MY_PROF_TITLE}','{MY_PROF_TGT}','my_profile',$template_sys_menu_spacer);
addbutton($sys_menu_buttons,'{ADM_MODE_LNK}','{ADM_MODE_TITLE}','{ADM_MODE_TGT}','enter_admin_mode',$template_sys_menu_spacer);
addbutton($sys_menu_buttons,'{USR_MODE_LNK}','{USR_MODE_TITLE}','{USR_MODE_TGT}','leave_admin_mode',$template_sys_menu_spacer);
addbutton($sys_menu_buttons,'{UPL_PIC_LNK}','{UPL_PIC_TITLE}','{UPL_PIC_TGT}','upload_pic',$template_sys_menu_spacer);
addbutton($sys_menu_buttons,'{REGISTER_LNK}','{REGISTER_TITLE}','{REGISTER_TGT}','register',$template_sys_menu_spacer);
addbutton($sys_menu_buttons,'{FAQ_LNK}','{FAQ_TITLE}','{FAQ_TGT}','faq',$template_sys_menu_spacer);
addbutton($sys_menu_buttons,'{LOGIN_LNK}','{LOGIN_TITLE}','{LOGIN_TGT}','login','');
addbutton($sys_menu_buttons,'{LOGOUT_LNK}','{LOGOUT_TITLE}','{LOGOUT_TGT}','logout','');
// Login and Logout don't have a spacer as only one is shown, and either would be the last option.
and the plugin works a treat to remove a number of these buttons. However, I would also like to remove the My Profile button.
Am I right in assuming that the way to do that is to change this section in my theme.php
// HTML template for gallery admin menu
$template_gallery_admin_menu = <<<EOT
<div align="center">
<table cellpadding="0" cellspacing="1">
<tr>
<!-- BEGIN admin_approval -->
<td class="admin_menu" id="admin_menu_anim"><a href="editpics.php?mode=upload_approval" title="{UPL_APP_TITLE}">{UPL_APP_LNK}</a></td>
<!-- END admin_approval -->
<td class="admin_menu"><a href="admin.php" title="{ADMIN_TITLE}">{ADMIN_LNK}</a></td>
<td class="admin_menu"><a href="catmgr.php" title="{CATEGORIES_TITLE}">{CATEGORIES_LNK}</a></td>
<td class="admin_menu"><a href="albmgr.php{CATL}" title="{ALBUMS_TITLE}">{ALBUMS_LNK}</a></td>
<td class="admin_menu"><a href="groupmgr.php" title="{GROUPS_TITLE}">{GROUPS_LNK}</a></td>
<td class="admin_menu"><a href="usermgr.php" title="{USERS_TITLE}">{USERS_LNK}</a></td>
<td class="admin_menu"><a href="banning.php" title="{BAN_TITLE}">{BAN_LNK}</a></td>
<td class="admin_menu"><a href="reviewcom.php" title="{COMMENTS_TITLE}">{COMMENTS_LNK}</a></td>
<!-- BEGIN log_ecards -->
<td class="admin_menu"><a href="db_ecard.php" title="{DB_ECARD_TITLE}">{DB_ECARD_LNK}</a></td>
<!-- END log_ecards -->
<td class="admin_menu"><a href="picmgr.php" title="{PICTURES_TITLE}">{PICTURES_LNK}</a></td>
<td class="admin_menu"><a href="searchnew.php" title="{SEARCHNEW_TITLE}">{SEARCHNEW_LNK}</a></td>
<td class="admin_menu"><a href="util.php" title="{UTIL_TITLE}">{UTIL_LNK}</a></td>
<!-- <td class="admin_menu"><a href="profile.php?op=edit_profile" title="{MY_PROF_TITLE}">{MY_PROF_LNK}</a></td>-->
<!-- BEGIN documentation -->
<td class="admin_menu"><a href="{DOCUMENTATION_HREF}" title="{DOCUMENTATION_TITLE}" target="cpg_documentation">{DOCUMENTATION_LNK}</a></td>
<!-- END documentation -->
</tr>
</table>
</div>
EOT;
// HTML template for user admin menu
$template_user_admin_menu = <<<EOT
<div align="center">
<table cellpadding="0" cellspacing="1">
<tr>
<td class="admin_menu"><a href="albmgr.php" title="{ALBMGR_TITLE}">{ALBMGR_LNK}</a></td>
<td class="admin_menu"><a href="modifyalb.php" title="{MODIFYALB_TITLE}">{MODIFYALB_LNK}</a></td>
<!-- <td class="admin_menu"><a href="profile.php?op=edit_profile" title="{MY_PROF_TITLE}">{MY_PROF_LNK}</a></td>-->
<td class="admin_menu"><a href="picmgr.php" title="{PICTURES_TITLE}">{PICTURES_LNK}</a></td>
</tr>
</table>
</div>
EOT;
and comment the My Profile link out as I have done it? It does work, but I am just unsure whether the plugin would have been able to handle it as well.