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I have 2 websites configured in a single instance, where i wanted to configure separate search indexes of solr for each website.

Even if you have multiple sites on the same Sitecore instance, you can have only a single Solr Server with different cores.

First, you need to create a custom solr index configuration file for each site. Example:

For Site A

<?xml version="1.0" encoding="utf-8" ?>

<configuration xmlns:patch="http://www.sitecore.net/xmlconfig/">

  <sitecore>

    <contentSearch>

      <configuration type="Sitecore.ContentSearch.ContentSearchConfiguration, Sitecore.ContentSearch">

        <indexes hint="list:AddIndex">

          <index id="sitecore_web_index_site_a" type="Sitecore.ContentSearch.SolrProvider.SolrSearchIndex, Sitecore.ContentSearch.SolrProvider">

            <param desc="name">$(id)</param>

            <param desc="core">$(id)</param>

            <param desc="propertyStore" ref="contentSearch/indexConfigurations/databasePropertyStore" param1="$(id)" />

            <configuration ref="contentSearch/indexConfigurations/defaultSolrIndexConfiguration" />

            <strategies hint="list:AddStrategy">

              <strategy ref="contentSearch/indexConfigurations/indexUpdateStrategies/onPublishEndAsync" />

            </strategies>

            <locations hint="list:AddCrawler">

              <crawler type="Sitecore.ContentSearch.SitecoreItemCrawler, Sitecore.ContentSearch">

                <Database>web</Database>

                <Root>/sitecore/content/Site A</Root>

              </crawler>

            </locations>

            <enableItemLanguageFallback>false</enableItemLanguageFallback>

            <enableFieldLanguageFallback>false</enableFieldLanguageFallback>

          </index>

        </indexes>

      </configuration>

    </contentSearch>

  </sitecore>

</configuration>

For Site B

<?xml version="1.0" encoding="utf-8" ?>

<configuration xmlns:patch="http://www.sitecore.net/xmlconfig/">

  <sitecore>

    <contentSearch>

      <configuration type="Sitecore.ContentSearch.ContentSearchConfiguration, Sitecore.ContentSearch">

        <indexes hint="list:AddIndex">

          <index id="sitecore_web_index_site_b" type="Sitecore.ContentSearch.SolrProvider.SolrSearchIndex, Sitecore.ContentSearch.SolrProvider">

            <param desc="name">$(id)</param>

            <param desc="core">$(id)</param>

            <param desc="propertyStore" ref="contentSearch/indexConfigurations/databasePropertyStore" param1="$(id)" />

            <configuration ref="contentSearch/indexConfigurations/defaultSolrIndexConfiguration" />

            <strategies hint="list:AddStrategy">

              <strategy ref="contentSearch/indexConfigurations/indexUpdateStrategies/onPublishEndAsync" />

            </strategies>

            <locations hint="list:AddCrawler">

              <crawler type="Sitecore.ContentSearch.SitecoreItemCrawler, Sitecore.ContentSearch">

                <Database>web</Database>

                <Root>/sitecore/content/Site B</Root>

              </crawler>

            </locations>

            <enableItemLanguageFallback>false</enableItemLanguageFallback>

            <enableFieldLanguageFallback>false</enableFieldLanguageFallback>

          </index>

        </indexes>

      </configuration>

    </contentSearch>

  </sitecore>

</configuration>

Second, once you have your configuration files setup, you need to create the cores of those sites on the Solr Server with the same name as you mentioned in the configuration file. Based on the configuration snippet above, the cores in Solr will be named: sitecore_web_index_site_a and sitecore_web_index_site_b.

Note that you need to change the root of the crawler so that it points to the Site path. Moreover, you can take the Sitecore default solr indexes for master, web and core as an example.