Linux IPv6 HOWTO
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7.3. Removing an IPv6 route through a gateway

Not so often needed manually, mostly done by network configure scripts on shutdown (full or per interface)

7.3.1. Using "ip"

Usage: 

# /sbin/ip -6 route del <ipv6network>/<prefixlength> via <ipv6address>
ΒΌ [dev <device>]

Example: 

# /sbin/ip -6 route del 2000::/3 via 3ffe:ffff:0:f101::1

7.3.2. Using "route"

Usage: 

# /sbin/route -A inet6 del <network>/<prefixlength> [dev <device>]

Example for removing upper added route again: 

# /sbin/route -A inet6 del 2000::/3 gw 3ffe:ffff:0:f101::1
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